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Experiment: ATHB1 mutant response to methyl jasmonate

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-572

ATHB1 is a member of the HD-ZIP I family of transcription factors, peculiar to plants. To understand the functional role of ATHB-1 in Arabidopsis, we identified athb1-1 and athb1-2 loss-of-function insertional mutants. Both alleles do not show any phenotypic alteration respect to overall size and morphology under our growth conditions, likely due to a functional redundancy within the HD-ZIP I family. However, gene expression analysis suggests that ATHB1 could take part in plant responses to environmental stresses. In fact, ATHB1 expression is affected by flooding and wounding, and by ethylene and methyl jasmonate (MeJA). Moreover, although wild type and mutant plants were clearly impaired by MeJA in a dose dependent manner, both athb1 alleles were less affected and showed a reduced rate of seedling mortality.In order to investigate the role of ATHB-1 in the MeJA response at genomic level, a transcriptome analysis will be performed on wild type (Ler) and athb1-2 plants treated with 30 μM MeJA. To this end, RNA samples have been prepared from 1 week-old plants treated with MeJA or ethanol (mock) for 1 hour and 4 hour.

About the Experimenter

Name: Simona Baima
Head of Lab Name: Giorgio Morelli
Lab:
Address:Istituto Nazionale di Ricerca per gli Alimenti e la Nutrizione (INRAN)
Via Ardeatina 546, Rome, Roma, , 00178, ITALY
Postcode:
Country:
 
Telephone Number: +39-06-51494453
Fax Number: +39-06-51494550

All of the data available in this website/database is free, and you are free to do whatever you please with it. If you intend to publish work based on any of this data, please acknowledge us, contact the experimenter above, and either acknowledge them or use them as co-authors in the work.

About this Experiment

Experiment Type: compound_based_treatment
Number of Slides:24
 
Experimental Parameters:
parametercompound_based_treatment
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Baima: athb1 mutant response to methyl jasmonate

Slide: Baima_572-1_Ler_EtOH_1h_Rep1_ATH1

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-1_Ler_EtOH_1h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-1_Ler_EtOH_1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 7 dpg
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction.
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.379421
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.455416
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.006092
Spike_AFFX-r2-Bs-dap_5_signal43.670826
NoiseAvg:2.70,Std:0.09,Min:2.4,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal17.772623
#P15774
Spike_AFFX-r2-Bs-phe_M_signal20.879526
Corner-Avg:12756,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal68.684654
Spike_AFFX-r2-Ec-bioB_3_signal52.713512
Spike_AFFX-r2-Bs-lys_M_signal6.099487
Spike_AFFX-r2-P1-cre_3_signal3786.428711
Spike_AFFX-r2-Bs-lys_3-5-ratio1.927602
Spike_AFFX-r2-Bs-dap_M_signal133.930481
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.158573
Spike_AFFX-r2-Ec-bioB_avg-signal57.930836
Spike_AFFX-r2-Bs-thr_avg-signal30.030067
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal499.613861
Spike_AFFX-r2-Bs-phe_5_signal19.306290
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal810.273071
RawQ2.393833
Spike_AFFX-r2-Bs-lys_5_signal9.901233
Signal(A)3.012367
%A29.302937
Signal(All)142.570343
Corner+Avg:211,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal226.202011
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal24.707945
Spike_AFFX-r2-Ec-bioD_avg-signal654.943481
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.153877
Spike_AFFX-r2-Bs-lys_avg-signal11.695453
Spike_AFFX-r2-P1-cre_avg-signal3194.020752
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.543183
Spike_AFFX-r2-Bs-thr_3_signal38.363503
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal21.631254
Spike_AFFX-r2-Bs-dap_3_signal165.255844
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.621799
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal194.568985
#M352
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal19.085638
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.162580
Spike_AFFX-r2-Bs-thr_M_signal33.954082
Signal(P)204.604080
Spike_AFFX-r2-Bs-phe_3-5-ratio1.279787
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8150,Count:9
Spike_AFFX-r2-P1-cre_5_signal2601.612793
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6684
Signal(M)12.699431
BackgroundAvg:55.33,Std:0.71,Min:53.3,Max:58.0
Spike_AFFX-r2-Ec-bioC_avg-signal210.385498
Spike_AFFX-r2-Bs-dap_avg-signal114.285728
Spike_AFFX-r2-Bs-dap_3-5-ratio3.784125
Spike_AFFX-r2-Ec-bioB_5_signal52.394341
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.379421
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-2_athb1-2_EtOH_1h_Rep1_ATH1

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-2_athb1-2_EtOH_1h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-2_athb1-2_EtOH_1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: athb1-2
Stock Code:
Genetic Background: Ler-0
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: Transposon knock out mutation in AT3g01470
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample is the control: mock treatment for 1h (This is the first of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.395607
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.015584
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.042737
Spike_AFFX-r2-Bs-dap_5_signal35.754166
NoiseAvg:3.01,Std:0.13,Min:2.7,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal17.270067
#P15644
Spike_AFFX-r2-Bs-phe_M_signal16.399042
Corner-Avg:11058,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal71.237518
Spike_AFFX-r2-Ec-bioB_3_signal57.816441
Spike_AFFX-r2-Bs-lys_M_signal7.608132
Spike_AFFX-r2-P1-cre_3_signal2708.885986
Spike_AFFX-r2-Bs-lys_3-5-ratio1.514220
Spike_AFFX-r2-Bs-dap_M_signal128.756500
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.956035
Spike_AFFX-r2-Ec-bioB_avg-signal61.500248
Spike_AFFX-r2-Bs-thr_avg-signal47.685944
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal525.275879
Spike_AFFX-r2-Bs-phe_5_signal20.665627
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal845.559265
RawQ2.739349
Spike_AFFX-r2-Bs-lys_5_signal16.935619
Signal(A)2.979179
%A29.789566
Signal(All)140.367615
Corner+Avg:173,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal200.296280
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal18.056826
Spike_AFFX-r2-Ec-bioD_avg-signal685.417603
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.583954
Spike_AFFX-r2-Bs-lys_avg-signal16.729334
Spike_AFFX-r2-P1-cre_avg-signal2688.101563
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.626480
Spike_AFFX-r2-Bs-thr_3_signal68.320984
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.373831
Spike_AFFX-r2-Bs-dap_3_signal146.841690
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.609743
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal190.079346
#M371
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal25.644251
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.053751
Spike_AFFX-r2-Bs-thr_M_signal57.466785
Signal(P)203.071167
Spike_AFFX-r2-Bs-phe_3-5-ratio0.873761
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8039,Count:9
Spike_AFFX-r2-P1-cre_5_signal2667.317139
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6795
Signal(M)12.659326
BackgroundAvg:65.04,Std:0.77,Min:63.5,Max:67.0
Spike_AFFX-r2-Ec-bioC_avg-signal195.187805
Spike_AFFX-r2-Bs-dap_avg-signal103.784119
Spike_AFFX-r2-Bs-dap_3-5-ratio4.106981
Spike_AFFX-r2-Ec-bioB_5_signal55.446796
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.395607
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-3_Ler_MeJA_1h_Rep1_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-3_Ler_MeJA_1h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-3_Ler_MeJA_1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 ;mol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample has been treated with 30 μM MeJA for 1h (This is the first of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.353962
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.221438
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.017349
Spike_AFFX-r2-Bs-dap_5_signal33.768829
NoiseAvg:3.15,Std:0.11,Min:2.7,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.834513
#P15624
Spike_AFFX-r2-Bs-phe_M_signal14.826468
Corner-Avg:12899,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal75.769798
Spike_AFFX-r2-Ec-bioB_3_signal64.050934
Spike_AFFX-r2-Bs-lys_M_signal4.876846
Spike_AFFX-r2-P1-cre_3_signal2902.902832
Spike_AFFX-r2-Bs-lys_3-5-ratio2.268945
Spike_AFFX-r2-Bs-dap_M_signal88.425636
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.804915
Spike_AFFX-r2-Ec-bioB_avg-signal67.593140
Spike_AFFX-r2-Bs-thr_avg-signal26.190329
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal487.795532
Spike_AFFX-r2-Bs-phe_5_signal13.710150
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1005.384399
RawQ2.695793
Spike_AFFX-r2-Bs-lys_5_signal11.743565
Signal(A)2.970686
%A29.829021
Signal(All)139.148987
Corner+Avg:193,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal185.006119
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal17.912218
Spike_AFFX-r2-Ec-bioD_avg-signal746.589966
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.496277
Spike_AFFX-r2-Bs-lys_avg-signal14.421971
Spike_AFFX-r2-P1-cre_avg-signal2639.765625
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.674704
Spike_AFFX-r2-Bs-thr_3_signal35.999718
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal15.482945
Spike_AFFX-r2-Bs-dap_3_signal118.855141
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.061078
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal201.302185
#M382
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.645504
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.919047
Spike_AFFX-r2-Bs-thr_M_signal29.736755
Signal(P)201.576843
Spike_AFFX-r2-Bs-phe_3-5-ratio1.306493
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10860,Count:9
Spike_AFFX-r2-P1-cre_5_signal2376.628174
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6804
Signal(M)11.359541
BackgroundAvg:66.42,Std:0.78,Min:64.6,Max:68.5
Spike_AFFX-r2-Ec-bioC_avg-signal193.154144
Spike_AFFX-r2-Bs-dap_avg-signal80.349869
Spike_AFFX-r2-Bs-dap_3-5-ratio3.519670
Spike_AFFX-r2-Ec-bioB_5_signal62.958679
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.353962
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-4_athb1-2_MeJA_1h_Rep1_ATH1

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-4_athb1-2_MeJA_1h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-4_athb1-2_MeJA_1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: athb1-2
Stock Code:
Genetic Background: Ler-0
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: Transposon knock out mutation in AT3g01470
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample has been treated with 30 μM MeJA for 1h (This is the first of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.348397
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.322089
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.092738
Spike_AFFX-r2-Bs-dap_5_signal41.455379
NoiseAvg:3.11,Std:0.09,Min:2.9,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.900469
#P15523
Spike_AFFX-r2-Bs-phe_M_signal22.503527
Corner-Avg:11588,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal60.329948
Spike_AFFX-r2-Ec-bioB_3_signal54.409588
Spike_AFFX-r2-Bs-lys_M_signal12.945761
Spike_AFFX-r2-P1-cre_3_signal2990.728516
Spike_AFFX-r2-Bs-lys_3-5-ratio2.118866
Spike_AFFX-r2-Bs-dap_M_signal111.085808
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.275026
Spike_AFFX-r2-Ec-bioB_avg-signal54.843838
Spike_AFFX-r2-Bs-thr_avg-signal29.912338
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal470.102478
Spike_AFFX-r2-Bs-phe_5_signal17.313669
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal844.146851
RawQ2.776223
Spike_AFFX-r2-Bs-lys_5_signal10.818890
Signal(A)2.911747
%A30.144674
Signal(All)139.765457
Corner+Avg:178,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal181.185913
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal18.979603
Spike_AFFX-r2-Ec-bioD_avg-signal657.124634
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.053482
Spike_AFFX-r2-Bs-lys_avg-signal15.562809
Spike_AFFX-r2-P1-cre_avg-signal2626.425781
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.801841
Spike_AFFX-r2-Bs-thr_3_signal38.449005
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal19.598932
Spike_AFFX-r2-Bs-dap_3_signal89.648727
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.795666
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal174.881607
#M411
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal22.923779
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.036049
Spike_AFFX-r2-Bs-thr_M_signal34.387543
Signal(P)203.765671
Spike_AFFX-r2-Bs-phe_3-5-ratio1.096221
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10021,Count:9
Spike_AFFX-r2-P1-cre_5_signal2262.122803
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6876
Signal(M)12.103086
BackgroundAvg:66.16,Std:0.96,Min:64.0,Max:68.5
Spike_AFFX-r2-Ec-bioC_avg-signal178.033752
Spike_AFFX-r2-Bs-dap_avg-signal80.729973
Spike_AFFX-r2-Bs-dap_3-5-ratio2.162535
Spike_AFFX-r2-Ec-bioB_5_signal49.791973
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.348397
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-5_Ler_EtOH_4h_Rep1_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-5_Ler_EtOH_4h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-5_Ler_EtOH_4h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample is the control: mock treatment for 4h (This is the first of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.499948
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.018958
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.886960
Spike_AFFX-r2-Bs-dap_5_signal32.027893
NoiseAvg:3.04,Std:0.15,Min:2.7,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.532244
#P15359
Spike_AFFX-r2-Bs-phe_M_signal19.175764
Corner-Avg:10723,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal67.192558
Spike_AFFX-r2-Ec-bioB_3_signal50.427151
Spike_AFFX-r2-Bs-lys_M_signal7.593970
Spike_AFFX-r2-P1-cre_3_signal2360.231689
Spike_AFFX-r2-Bs-lys_3-5-ratio1.781623
Spike_AFFX-r2-Bs-dap_M_signal83.980644
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.075915
Spike_AFFX-r2-Ec-bioB_avg-signal58.157867
Spike_AFFX-r2-Bs-thr_avg-signal24.147469
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal405.148712
Spike_AFFX-r2-Bs-phe_5_signal13.475223
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal852.727966
RawQ2.788075
Spike_AFFX-r2-Bs-lys_5_signal11.748446
Signal(A)3.903112
%A30.868040
Signal(All)141.730469
Corner+Avg:156,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal193.565201
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal16.387722
Spike_AFFX-r2-Ec-bioD_avg-signal628.938354
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.334503
Spike_AFFX-r2-Bs-lys_avg-signal13.424571
Spike_AFFX-r2-P1-cre_avg-signal2338.275146
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.797457
Spike_AFFX-r2-Bs-thr_3_signal30.700785
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal16.346235
Spike_AFFX-r2-Bs-dap_3_signal92.714142
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.104728
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal157.870941
#M410
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal20.931297
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.226098
Spike_AFFX-r2-Bs-thr_M_signal34.209381
Signal(P)208.319031
Spike_AFFX-r2-Bs-phe_3-5-ratio1.216137
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11230,Count:9
Spike_AFFX-r2-P1-cre_5_signal2316.318604
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7041
Signal(M)14.190262
BackgroundAvg:65.04,Std:0.79,Min:63.0,Max:67.1
Spike_AFFX-r2-Ec-bioC_avg-signal175.718079
Spike_AFFX-r2-Bs-dap_avg-signal69.574226
Spike_AFFX-r2-Bs-dap_3-5-ratio2.894794
Spike_AFFX-r2-Ec-bioB_5_signal56.853897
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.499948
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-6_athb1-2_EtOH_4h_Rep1_ATH1

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-6_athb1-2_EtOH_4h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-6_athb1-2_EtOH_4h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: athb1-2
Stock Code:
Genetic Background: Ler-0
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: Transposon knock out mutation in AT3g01470
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample is the control: mock treatment for 4h (This is the first of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.448536
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.096700
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.290049
Spike_AFFX-r2-Bs-dap_5_signal49.518494
NoiseAvg:3.04,Std:0.11,Min:2.7,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.803980
#P15484
Spike_AFFX-r2-Bs-phe_M_signal20.065958
Corner-Avg:17850,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal68.370651
Spike_AFFX-r2-Ec-bioB_3_signal59.037781
Spike_AFFX-r2-Bs-lys_M_signal9.458809
Spike_AFFX-r2-P1-cre_3_signal2864.239746
Spike_AFFX-r2-Bs-lys_3-5-ratio1.608046
Spike_AFFX-r2-Bs-dap_M_signal129.052429
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.989509
Spike_AFFX-r2-Ec-bioB_avg-signal57.724140
Spike_AFFX-r2-Bs-thr_avg-signal38.731838
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal468.367279
Spike_AFFX-r2-Bs-phe_5_signal22.364260
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal923.980835
RawQ2.748175
Spike_AFFX-r2-Bs-lys_5_signal16.373508
Signal(A)3.680745
%A30.346340
Signal(All)142.269485
Corner+Avg:273,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal199.967239
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal42.288441
Spike_AFFX-r2-Ec-bioD_avg-signal696.174072
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.882507
Spike_AFFX-r2-Bs-lys_avg-signal17.387224
Spike_AFFX-r2-P1-cre_avg-signal2737.964355
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.771153
Spike_AFFX-r2-Bs-thr_3_signal50.235657
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal28.239553
Spike_AFFX-r2-Bs-dap_3_signal147.352646
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.972770
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal159.359314
#M404
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.329353
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.254820
Spike_AFFX-r2-Bs-thr_M_signal49.155880
Signal(P)207.555389
Spike_AFFX-r2-Bs-phe_3-5-ratio1.890894
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16883,Count:9
Spike_AFFX-r2-P1-cre_5_signal2611.689209
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6922
Signal(M)14.606718
BackgroundAvg:63.76,Std:1.06,Min:61.4,Max:66.4
Spike_AFFX-r2-Ec-bioC_avg-signal179.663269
Spike_AFFX-r2-Bs-dap_avg-signal108.641197
Spike_AFFX-r2-Bs-dap_3-5-ratio2.975709
Spike_AFFX-r2-Ec-bioB_5_signal45.763985
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.448536
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-7_Ler_MeJA_4h_Rep1_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-7_Ler_MeJA_4h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-7_Ler_MeJA_4h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample has been treated with 30 μM MeJA for 4h (This is the first of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.245866
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.275167
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.248149
Spike_AFFX-r2-Bs-dap_5_signal46.827858
NoiseAvg:3.78,Std:0.18,Min:3.4,Max:4.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.961070
#P15847
Spike_AFFX-r2-Bs-phe_M_signal23.863159
Corner-Avg:20508,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal59.054386
Spike_AFFX-r2-Ec-bioB_3_signal56.061806
Spike_AFFX-r2-Bs-lys_M_signal10.773837
Spike_AFFX-r2-P1-cre_3_signal2484.855225
Spike_AFFX-r2-Bs-lys_3-5-ratio1.935592
Spike_AFFX-r2-Bs-dap_M_signal103.582977
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.309471
Spike_AFFX-r2-Ec-bioB_avg-signal53.344055
Spike_AFFX-r2-Bs-thr_avg-signal26.742598
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal378.486115
Spike_AFFX-r2-Bs-phe_5_signal14.086403
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal727.270752
RawQ2.988481
Spike_AFFX-r2-Bs-lys_5_signal14.782815
Signal(A)2.698268
%A28.838228
Signal(All)136.003723
Corner+Avg:322,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal155.492569
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.053230
Spike_AFFX-r2-Ec-bioD_avg-signal552.878418
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.473915
Spike_AFFX-r2-Bs-lys_avg-signal18.056715
Spike_AFFX-r2-P1-cre_avg-signal2216.753174
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.687856
Spike_AFFX-r2-Bs-thr_3_signal36.275345
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal22.000931
Spike_AFFX-r2-Bs-dap_3_signal146.903290
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.921526
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal139.313080
#M385
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.613493
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.116138
Spike_AFFX-r2-Bs-thr_M_signal32.991383
Signal(P)194.349274
Spike_AFFX-r2-Bs-phe_3-5-ratio1.991511
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:18193,Count:9
Spike_AFFX-r2-P1-cre_5_signal1948.651001
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6578
Signal(M)12.058563
BackgroundAvg:72.37,Std:1.25,Min:69.3,Max:75.5
Spike_AFFX-r2-Ec-bioC_avg-signal147.402832
Spike_AFFX-r2-Bs-dap_avg-signal99.104706
Spike_AFFX-r2-Bs-dap_3-5-ratio3.137092
Spike_AFFX-r2-Ec-bioB_5_signal44.915962
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.245866
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-8_athb1-2_MeJA_4h_Rep1_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-8_athb1-2_MeJA_4h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-8_athb1-2_MeJA_4h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: athb1-2
Stock Code:
Genetic Background: Ler-0
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: Transposon knock out mutation in AT3g01470
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample has been treated with 30 μM MeJA for 4h (This is the first of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.41628
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.210547
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.565130
Spike_AFFX-r2-Bs-dap_5_signal34.382217
NoiseAvg:3.34,Std:0.13,Min:3.0,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.211076
#P15236
Spike_AFFX-r2-Bs-phe_M_signal19.931667
Corner-Avg:16623,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal77.481544
Spike_AFFX-r2-Ec-bioB_3_signal52.011478
Spike_AFFX-r2-Bs-lys_M_signal9.900772
Spike_AFFX-r2-P1-cre_3_signal2830.781982
Spike_AFFX-r2-Bs-lys_3-5-ratio2.296352
Spike_AFFX-r2-Bs-dap_M_signal99.250824
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.721064
Spike_AFFX-r2-Ec-bioB_avg-signal54.241482
Spike_AFFX-r2-Bs-thr_avg-signal30.309982
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal466.935944
Spike_AFFX-r2-Bs-phe_5_signal18.857948
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal831.072083
RawQ2.848855
Spike_AFFX-r2-Bs-lys_5_signal12.415563
Signal(A)3.605372
%A31.494959
Signal(All)140.633041
Corner+Avg:555,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal186.937805
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal27.014038
Spike_AFFX-r2-Ec-bioD_avg-signal649.004028
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.795265
Spike_AFFX-r2-Bs-lys_avg-signal16.942278
Spike_AFFX-r2-P1-cre_avg-signal2584.607422
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.709776
Spike_AFFX-r2-Bs-thr_3_signal41.717133
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal21.934549
Spike_AFFX-r2-Bs-dap_3_signal122.508598
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.779842
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal160.207016
#M390
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.510500
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.166852
Spike_AFFX-r2-Bs-thr_M_signal38.001740
Signal(P)208.497864
Spike_AFFX-r2-Bs-phe_3-5-ratio1.432501
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16901,Count:9
Spike_AFFX-r2-P1-cre_5_signal2338.432861
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7184
Signal(M)13.500572
BackgroundAvg:68.57,Std:0.60,Min:67.2,Max:70.0
Spike_AFFX-r2-Ec-bioC_avg-signal173.572418
Spike_AFFX-r2-Bs-dap_avg-signal85.380554
Spike_AFFX-r2-Bs-dap_3-5-ratio3.563138
Spike_AFFX-r2-Ec-bioB_5_signal33.231415
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.416280
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-9_Ler_EtOH_1h_Rep2_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-9_Ler_EtOH_1h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-9_Ler_EtOH_1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample is the control: mock treatment for 1h (This is the second of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.454307
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.318593
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.473421
Spike_AFFX-r2-Bs-dap_5_signal64.127014
NoiseAvg:2.55,Std:0.10,Min:2.3,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal24.936005
#P15481
Spike_AFFX-r2-Bs-phe_M_signal38.082733
Corner-Avg:17976,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal83.676682
Spike_AFFX-r2-Ec-bioB_3_signal68.635056
Spike_AFFX-r2-Bs-lys_M_signal14.356987
Spike_AFFX-r2-P1-cre_3_signal3113.319092
Spike_AFFX-r2-Bs-lys_3-5-ratio2.019217
Spike_AFFX-r2-Bs-dap_M_signal158.155289
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.055486
Spike_AFFX-r2-Ec-bioB_avg-signal66.297951
Spike_AFFX-r2-Bs-thr_avg-signal53.100266
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal525.142151
Spike_AFFX-r2-Bs-phe_5_signal28.612038
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1085.312622
RawQ2.370758
Spike_AFFX-r2-Bs-lys_5_signal19.571367
Signal(A)3.112291
%A30.526085
Signal(All)141.079529
Corner+Avg:272,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal161.425507
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal32.696815
Spike_AFFX-r2-Ec-bioD_avg-signal805.227417
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.869354
Spike_AFFX-r2-Bs-lys_avg-signal24.482397
Spike_AFFX-r2-P1-cre_avg-signal2737.205566
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.604559
Spike_AFFX-r2-Bs-thr_3_signal76.191620
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal33.130527
Spike_AFFX-r2-Bs-dap_3_signal205.808395
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.066703
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal193.754196
#M366
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal39.518833
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.833146
Spike_AFFX-r2-Bs-thr_M_signal58.173168
Signal(P)206.141479
Spike_AFFX-r2-Bs-phe_3-5-ratio1.142764
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13560,Count:9
Spike_AFFX-r2-P1-cre_5_signal2361.092041
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6963
Signal(M)13.870950
BackgroundAvg:51.64,Std:0.90,Min:50.2,Max:54.4
Spike_AFFX-r2-Ec-bioC_avg-signal177.589844
Spike_AFFX-r2-Bs-dap_avg-signal142.696899
Spike_AFFX-r2-Bs-dap_3-5-ratio3.209387
Spike_AFFX-r2-Ec-bioB_5_signal46.582108
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.454307
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-10_athb1-2_EtOH_1h_Rep2_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-10_athb1-2_EtOH_1h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-10_athb1-2_EtOH_1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: athb1-2
Stock Code:
Genetic Background: Ler-0
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: Transposon knock out mutation in AT3g01470
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample is the control: mock treatment for 1h (This is the second of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.471032
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.926206
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.053469
Spike_AFFX-r2-Bs-dap_5_signal39.773418
NoiseAvg:2.46,Std:0.07,Min:2.2,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.923979
#P15382
Spike_AFFX-r2-Bs-phe_M_signal24.500154
Corner-Avg:11714,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal84.584892
Spike_AFFX-r2-Ec-bioB_3_signal61.884808
Spike_AFFX-r2-Bs-lys_M_signal12.529723
Spike_AFFX-r2-P1-cre_3_signal2764.784912
Spike_AFFX-r2-Bs-lys_3-5-ratio1.010105
Spike_AFFX-r2-Bs-dap_M_signal124.909416
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.585750
Spike_AFFX-r2-Ec-bioB_avg-signal68.404518
Spike_AFFX-r2-Bs-thr_avg-signal31.475021
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal518.137939
Spike_AFFX-r2-Bs-phe_5_signal15.384927
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal975.923584
RawQ2.425032
Spike_AFFX-r2-Bs-lys_5_signal18.115719
Signal(A)3.063043
%A30.793512
Signal(All)143.019989
Corner+Avg:178,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal203.120850
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal26.711267
Spike_AFFX-r2-Ec-bioD_avg-signal747.030762
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.435333
Spike_AFFX-r2-Bs-lys_avg-signal16.314741
Spike_AFFX-r2-P1-cre_avg-signal2874.924316
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.771153
Spike_AFFX-r2-Bs-thr_3_signal43.761177
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal22.198784
Spike_AFFX-r2-Bs-dap_3_signal142.808167
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.883521
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal209.945419
#M404
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.298784
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.967494
Spike_AFFX-r2-Bs-thr_M_signal33.739906
Signal(P)210.366440
Spike_AFFX-r2-Bs-phe_3-5-ratio1.736197
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10430,Count:9
Spike_AFFX-r2-P1-cre_5_signal2985.063965
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7024
Signal(M)12.165097
BackgroundAvg:52.57,Std:0.31,Min:51.4,Max:53.3
Spike_AFFX-r2-Ec-bioC_avg-signal206.533142
Spike_AFFX-r2-Bs-dap_avg-signal102.497002
Spike_AFFX-r2-Bs-dap_3-5-ratio3.590543
Spike_AFFX-r2-Ec-bioB_5_signal58.743858
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.471032
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-11_Ler_MeJA_1h_Rep2_ATH1

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-11_Ler_MeJA_1h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-11_Ler_MeJA_1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 ;mol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample has been treated with 30 μM MeJA for 1h (This is the second of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.408574
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.242447
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.321741
Spike_AFFX-r2-Bs-dap_5_signal42.617775
NoiseAvg:2.95,Std:0.09,Min:2.7,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal18.478203
#P15325
Spike_AFFX-r2-Bs-phe_M_signal22.869320
Corner-Avg:10795,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal81.930130
Spike_AFFX-r2-Ec-bioB_3_signal76.762482
Spike_AFFX-r2-Bs-lys_M_signal8.009283
Spike_AFFX-r2-P1-cre_3_signal3543.824219
Spike_AFFX-r2-Bs-lys_3-5-ratio1.300698
Spike_AFFX-r2-Bs-dap_M_signal118.775307
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.331216
Spike_AFFX-r2-Ec-bioB_avg-signal72.256470
Spike_AFFX-r2-Bs-thr_avg-signal31.335266
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal557.985901
Spike_AFFX-r2-Bs-phe_5_signal16.141254
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal999.454834
RawQ2.640115
Spike_AFFX-r2-Bs-lys_5_signal12.660628
Signal(A)2.965471
%A31.012714
Signal(All)140.653000
Corner+Avg:162,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal231.240448
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.578722
Spike_AFFX-r2-Ec-bioD_avg-signal778.720337
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.185448
Spike_AFFX-r2-Bs-lys_avg-signal12.379189
Spike_AFFX-r2-P1-cre_avg-signal3198.059570
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.801841
Spike_AFFX-r2-Bs-thr_3_signal43.076683
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal20.196432
Spike_AFFX-r2-Bs-dap_3_signal105.983490
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.791183
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal222.230499
#M411
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal16.467657
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.040543
Spike_AFFX-r2-Bs-thr_M_signal32.450912
Signal(P)207.660660
Spike_AFFX-r2-Bs-phe_3-5-ratio1.336868
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9865,Count:9
Spike_AFFX-r2-P1-cre_5_signal2852.294922
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7074
Signal(M)11.965430
BackgroundAvg:62.83,Std:0.48,Min:61.7,Max:64.2
Spike_AFFX-r2-Ec-bioC_avg-signal226.735474
Spike_AFFX-r2-Bs-dap_avg-signal89.125519
Spike_AFFX-r2-Bs-dap_3-5-ratio2.486838
Spike_AFFX-r2-Ec-bioB_5_signal58.076790
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.408574
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-12_athb1-2_MeJA_1h_Rep2_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-12_athb1-2_MeJA_1h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-12_athb1-2_MeJA_1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: athb1-2
Stock Code:
Genetic Background: Ler-0
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: Transposon knock out mutation in AT3g01470
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample has been treated with 30 μ;M MeJA for 1h (This is the second of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.484063
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.317967
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.892018
Spike_AFFX-r2-Bs-dap_5_signal44.400948
NoiseAvg:2.92,Std:0.12,Min:2.6,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal18.050556
#P14791
Spike_AFFX-r2-Bs-phe_M_signal21.885990
Corner-Avg:10493,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal81.704178
Spike_AFFX-r2-Ec-bioB_3_signal55.956821
Spike_AFFX-r2-Bs-lys_M_signal7.715760
Spike_AFFX-r2-P1-cre_3_signal3636.717773
Spike_AFFX-r2-Bs-lys_3-5-ratio1.229360
Spike_AFFX-r2-Bs-dap_M_signal115.143730
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.742538
Spike_AFFX-r2-Ec-bioB_avg-signal66.797188
Spike_AFFX-r2-Bs-thr_avg-signal34.478138
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal584.135559
Spike_AFFX-r2-Bs-phe_5_signal13.846048
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1206.651367
RawQ2.677860
Spike_AFFX-r2-Bs-lys_5_signal16.430342
Signal(A)3.880247
%A33.169662
Signal(All)144.891403
Corner+Avg:179,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal253.044998
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal24.733496
Spike_AFFX-r2-Ec-bioD_avg-signal895.393433
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.844368
Spike_AFFX-r2-Bs-lys_avg-signal14.781634
Spike_AFFX-r2-P1-cre_avg-signal3198.028320
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.985971
Spike_AFFX-r2-Bs-thr_3_signal49.504345
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal20.155176
Spike_AFFX-r2-Bs-dap_3_signal133.695633
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.065704
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal249.966339
#M453
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal20.198797
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.012316
Spike_AFFX-r2-Bs-thr_M_signal35.879520
Signal(P)221.001205
Spike_AFFX-r2-Bs-phe_3-5-ratio1.786322
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7988,Count:9
Spike_AFFX-r2-P1-cre_5_signal2759.338623
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7566
Signal(M)14.980260
BackgroundAvg:62.63,Std:0.45,Min:61.5,Max:64.4
Spike_AFFX-r2-Ec-bioC_avg-signal251.505676
Spike_AFFX-r2-Bs-dap_avg-signal97.746765
Spike_AFFX-r2-Bs-dap_3-5-ratio3.011099
Spike_AFFX-r2-Ec-bioB_5_signal62.730579
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.484063
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-13_Ler_EtOH_4h_Rep2_ATH1

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-13_Ler_EtOH_4h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-13_Ler_EtOH_4h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample is the control: mock treatment for 4h (This is the second of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.45204
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.133382
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.266020
Spike_AFFX-r2-Bs-dap_5_signal30.730581
NoiseAvg:2.82,Std:0.12,Min:2.6,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal18.006845
#P15087
Spike_AFFX-r2-Bs-phe_M_signal24.394802
Corner-Avg:11550,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal66.032593
Spike_AFFX-r2-Ec-bioB_3_signal51.575256
Spike_AFFX-r2-Bs-lys_M_signal8.212773
Spike_AFFX-r2-P1-cre_3_signal2655.248047
Spike_AFFX-r2-Bs-lys_3-5-ratio1.895003
Spike_AFFX-r2-Bs-dap_M_signal117.379379
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.460011
Spike_AFFX-r2-Ec-bioB_avg-signal52.781986
Spike_AFFX-r2-Bs-thr_avg-signal44.009899
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal497.626526
Spike_AFFX-r2-Bs-phe_5_signal18.731110
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal794.076294
RawQ2.541856
Spike_AFFX-r2-Bs-lys_5_signal12.789813
Signal(A)3.548805
%A31.933363
Signal(All)143.016830
Corner+Avg:188,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal158.196442
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal39.543480
Spike_AFFX-r2-Ec-bioD_avg-signal645.851440
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.142044
Spike_AFFX-r2-Bs-lys_avg-signal15.079774
Spike_AFFX-r2-P1-cre_avg-signal2499.006348
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.924595
Spike_AFFX-r2-Bs-thr_3_signal62.303890
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal27.556463
Spike_AFFX-r2-Bs-dap_3_signal147.526871
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.595727
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal182.805649
#M439
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.236736
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.865380
Spike_AFFX-r2-Bs-thr_M_signal51.718956
Signal(P)214.069916
Spike_AFFX-r2-Bs-phe_3-5-ratio2.111113
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9007,Count:9
Spike_AFFX-r2-P1-cre_5_signal2342.764648
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7284
Signal(M)15.243210
BackgroundAvg:58.55,Std:0.48,Min:57.3,Max:59.8
Spike_AFFX-r2-Ec-bioC_avg-signal170.501038
Spike_AFFX-r2-Bs-dap_avg-signal98.545616
Spike_AFFX-r2-Bs-dap_3-5-ratio4.800653
Spike_AFFX-r2-Ec-bioB_5_signal40.738110
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.452040
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-14_athb1-2_EtOH_4h_Rep2_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-14_athb1-2_EtOH_4h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-14_athb1-2_EtOH_4h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: athb1-2
Stock Code:
Genetic Background: Ler-0
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: Transposon knock out mutation in AT3g01470
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample is the control: mock treatment for 4h (This is the second of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.528743
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.950728
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.207375
Spike_AFFX-r2-Bs-dap_5_signal40.340233
NoiseAvg:2.71,Std:0.16,Min:2.3,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal14.291606
#P15001
Spike_AFFX-r2-Bs-phe_M_signal14.335617
Corner-Avg:10374,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal58.680321
Spike_AFFX-r2-Ec-bioB_3_signal47.536594
Spike_AFFX-r2-Bs-lys_M_signal9.534807
Spike_AFFX-r2-P1-cre_3_signal2611.650391
Spike_AFFX-r2-Bs-lys_3-5-ratio2.148479
Spike_AFFX-r2-Bs-dap_M_signal95.797127
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.653024
Spike_AFFX-r2-Ec-bioB_avg-signal48.529591
Spike_AFFX-r2-Bs-thr_avg-signal31.682915
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal434.386780
Spike_AFFX-r2-Bs-phe_5_signal30.398607
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal876.250061
RawQ2.545046
Spike_AFFX-r2-Bs-lys_5_signal12.290462
Signal(A)3.874184
%A32.327927
Signal(All)144.349579
Corner+Avg:170,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal161.830933
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.595982
Spike_AFFX-r2-Ec-bioD_avg-signal655.318420
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.765015
Spike_AFFX-r2-Bs-lys_avg-signal16.077023
Spike_AFFX-r2-P1-cre_avg-signal2679.325928
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.907058
Spike_AFFX-r2-Bs-thr_3_signal37.915981
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal22.443403
Spike_AFFX-r2-Bs-dap_3_signal172.031265
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.017212
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal148.867004
#M435
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.405800
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.087084
Spike_AFFX-r2-Bs-thr_M_signal42.841156
Signal(P)217.135880
Spike_AFFX-r2-Bs-phe_3-5-ratio0.743323
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8254,Count:9
Spike_AFFX-r2-P1-cre_5_signal2747.001465
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7374
Signal(M)15.610338
BackgroundAvg:58.02,Std:1.28,Min:55.7,Max:61.6
Spike_AFFX-r2-Ec-bioC_avg-signal155.348969
Spike_AFFX-r2-Bs-dap_avg-signal102.722878
Spike_AFFX-r2-Bs-dap_3-5-ratio4.264508
Spike_AFFX-r2-Ec-bioB_5_signal39.371853
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.528743
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-15_Ler_MeJA_4h_Rep2_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-15_Ler_MeJA_4h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-15_Ler_MeJA_4h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample has been treated with 30 μM MeJA for 4h (This is the second of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.443101
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.126104
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.281546
Spike_AFFX-r2-Bs-dap_5_signal41.037708
NoiseAvg:2.56,Std:0.06,Min:2.4,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal15.287222
#P15066
Spike_AFFX-r2-Bs-phe_M_signal21.931772
Corner-Avg:9673,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal64.474503
Spike_AFFX-r2-Ec-bioB_3_signal55.940067
Spike_AFFX-r2-Bs-lys_M_signal6.034630
Spike_AFFX-r2-P1-cre_3_signal2975.344238
Spike_AFFX-r2-Bs-lys_3-5-ratio2.184806
Spike_AFFX-r2-Bs-dap_M_signal128.387314
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.901312
Spike_AFFX-r2-Ec-bioB_avg-signal54.688343
Spike_AFFX-r2-Bs-thr_avg-signal42.362087
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal428.754974
Spike_AFFX-r2-Bs-phe_5_signal22.347315
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal828.699158
RawQ2.375260
Spike_AFFX-r2-Bs-lys_5_signal16.121641
Signal(A)3.249749
%A32.284084
Signal(All)142.734436
Corner+Avg:160,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal165.485535
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.528126
Spike_AFFX-r2-Ec-bioD_avg-signal628.727051
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.049980
Spike_AFFX-r2-Bs-lys_avg-signal19.126307
Spike_AFFX-r2-P1-cre_avg-signal2808.750977
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.665936
Spike_AFFX-r2-Bs-thr_3_signal59.640217
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal24.269072
Spike_AFFX-r2-Bs-dap_3_signal165.561462
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.932804
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal175.092392
#M380
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal35.222652
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.945133
Spike_AFFX-r2-Bs-thr_M_signal52.158821
Signal(P)214.175125
Spike_AFFX-r2-Bs-phe_3-5-ratio1.276580
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5961,Count:9
Spike_AFFX-r2-P1-cre_5_signal2642.157715
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7364
Signal(M)13.365019
BackgroundAvg:55.23,Std:0.81,Min:53.6,Max:57.4
Spike_AFFX-r2-Ec-bioC_avg-signal170.288971
Spike_AFFX-r2-Bs-dap_avg-signal111.662170
Spike_AFFX-r2-Bs-dap_3-5-ratio4.034374
Spike_AFFX-r2-Ec-bioB_5_signal43.650467
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.443101
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-16_athb1-2_MeJA_4h_Rep2_ATH1

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-16_athb1-2_MeJA_4h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-16_athb1-2_MeJA_4h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: athb1-2
Stock Code:
Genetic Background: Ler-0
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: Transposon knock out mutation in AT3g01470
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample has been treated with 30 μM MeJA for 4h (This is the second of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.369953
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.305016
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.137197
Spike_AFFX-r2-Bs-dap_5_signal65.812309
NoiseAvg:2.76,Std:0.06,Min:2.6,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal22.993994
#P15384
Spike_AFFX-r2-Bs-phe_M_signal24.633162
Corner-Avg:11329,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal67.272240
Spike_AFFX-r2-Ec-bioB_3_signal54.587494
Spike_AFFX-r2-Bs-lys_M_signal16.511841
Spike_AFFX-r2-P1-cre_3_signal3538.925781
Spike_AFFX-r2-Bs-lys_3-5-ratio1.823588
Spike_AFFX-r2-Bs-dap_M_signal148.597610
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.727318
Spike_AFFX-r2-Ec-bioB_avg-signal56.620502
Spike_AFFX-r2-Bs-thr_avg-signal45.865082
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal543.526062
Spike_AFFX-r2-Bs-phe_5_signal25.739302
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal938.857544
RawQ2.602157
Spike_AFFX-r2-Bs-lys_5_signal19.901594
Signal(A)2.742709
%A30.903112
Signal(All)142.468033
Corner+Avg:176,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal187.844513
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal29.851665
Spike_AFFX-r2-Ec-bioD_avg-signal741.191772
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.444107
Spike_AFFX-r2-Bs-lys_avg-signal24.235247
Spike_AFFX-r2-P1-cre_avg-signal3125.356445
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.652784
Spike_AFFX-r2-Bs-thr_3_signal62.711937
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal26.741377
Spike_AFFX-r2-Bs-dap_3_signal189.869537
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.727346
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal186.480972
#M377
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal36.292309
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.007312
Spike_AFFX-r2-Bs-thr_M_signal51.889317
Signal(P)209.695450
Spike_AFFX-r2-Bs-phe_3-5-ratio1.159770
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8203,Count:9
Spike_AFFX-r2-P1-cre_5_signal2711.787109
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7049
Signal(M)11.691916
BackgroundAvg:59.62,Std:0.72,Min:58.0,Max:61.4
Spike_AFFX-r2-Ec-bioC_avg-signal187.162750
Spike_AFFX-r2-Bs-dap_avg-signal134.759827
Spike_AFFX-r2-Bs-dap_3-5-ratio2.885015
Spike_AFFX-r2-Ec-bioB_5_signal48.001785
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.369953
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-17_Ler_EtOH_1h_Rep3_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-17_Ler_EtOH_1h_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-17_Ler_EtOH_1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μM;mol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample is the control: mock treatment for 1h (This is the third of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.248741
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.296209
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.951577
Spike_AFFX-r2-Bs-dap_5_signal34.459042
NoiseAvg:3.27,Std:0.09,Min:2.9,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal13.187042
#P15976
Spike_AFFX-r2-Bs-phe_M_signal10.723997
Corner-Avg:11767,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal61.969429
Spike_AFFX-r2-Ec-bioB_3_signal40.597961
Spike_AFFX-r2-Bs-lys_M_signal6.011539
Spike_AFFX-r2-P1-cre_3_signal2670.411133
Spike_AFFX-r2-Bs-lys_3-5-ratio1.437240
Spike_AFFX-r2-Bs-dap_M_signal88.664391
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.334609
Spike_AFFX-r2-Ec-bioB_avg-signal48.410427
Spike_AFFX-r2-Bs-thr_avg-signal23.362337
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal427.886505
Spike_AFFX-r2-Bs-phe_5_signal22.257614
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal729.965637
RawQ2.868105
Spike_AFFX-r2-Bs-lys_5_signal11.679502
Signal(A)2.278025
%A28.412977
Signal(All)136.451935
Corner+Avg:176,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal165.895340
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.541843
Spike_AFFX-r2-Ec-bioD_avg-signal578.926086
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.039459
Spike_AFFX-r2-Bs-lys_avg-signal11.492429
Spike_AFFX-r2-P1-cre_avg-signal2365.291016
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.547567
Spike_AFFX-r2-Bs-thr_3_signal30.786583
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.174484
Spike_AFFX-r2-Bs-dap_3_signal107.190353
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.705980
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal164.119171
#M353
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal16.786247
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.010822
Spike_AFFX-r2-Bs-thr_M_signal26.113388
Signal(P)193.656509
Spike_AFFX-r2-Bs-phe_3-5-ratio0.967842
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9958,Count:9
Spike_AFFX-r2-P1-cre_5_signal2060.170654
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6481
Signal(M)10.901362
BackgroundAvg:69.03,Std:0.73,Min:67.1,Max:71.6
Spike_AFFX-r2-Ec-bioC_avg-signal165.007263
Spike_AFFX-r2-Bs-dap_avg-signal76.771263
Spike_AFFX-r2-Bs-dap_3-5-ratio3.110660
Spike_AFFX-r2-Ec-bioB_5_signal42.663887
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.248741
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-18_athb1-2_EtOH_1h_Rep3_ATH1

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-18_athb1-2_EtOH_1h_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-18_athb1-2_EtOH_1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: athb1-2
Stock Code:
Genetic Background: Ler-0
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: Transposon knock out mutation in AT3g01470
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample is the control: mock treatment for 1h (This is the third of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.341558
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.210131
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.098908
Spike_AFFX-r2-Bs-dap_5_signal21.059746
NoiseAvg:2.94,Std:0.10,Min:2.7,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal9.058434
#P15598
Spike_AFFX-r2-Bs-phe_M_signal10.957993
Corner-Avg:12589,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal75.352211
Spike_AFFX-r2-Ec-bioB_3_signal71.011925
Spike_AFFX-r2-Bs-lys_M_signal5.956719
Spike_AFFX-r2-P1-cre_3_signal3610.886963
Spike_AFFX-r2-Bs-lys_3-5-ratio2.679104
Spike_AFFX-r2-Bs-dap_M_signal61.426311
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.580313
Spike_AFFX-r2-Ec-bioB_avg-signal70.328201
Spike_AFFX-r2-Bs-thr_avg-signal17.957525
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal598.703125
Spike_AFFX-r2-Bs-phe_5_signal8.681057
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1015.485962
RawQ2.529653
Spike_AFFX-r2-Bs-lys_5_signal6.859490
Signal(A)2.737618
%A30.013153
Signal(All)142.198074
Corner+Avg:198,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal236.091599
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal9.413275
Spike_AFFX-r2-Ec-bioD_avg-signal807.094543
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.382286
Spike_AFFX-r2-Bs-lys_avg-signal10.397832
Spike_AFFX-r2-P1-cre_avg-signal3297.384521
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.604559
Spike_AFFX-r2-Bs-thr_3_signal23.373594
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal9.684108
Spike_AFFX-r2-Bs-dap_3_signal74.055740
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.696143
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal227.814224
#M366
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.377287
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.036334
Spike_AFFX-r2-Bs-thr_M_signal21.440544
Signal(P)206.467773
Spike_AFFX-r2-Bs-phe_3-5-ratio1.084347
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9707,Count:9
Spike_AFFX-r2-P1-cre_5_signal2983.882080
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6846
Signal(M)11.781741
BackgroundAvg:60.73,Std:0.70,Min:58.4,Max:62.7
Spike_AFFX-r2-Ec-bioC_avg-signal231.952911
Spike_AFFX-r2-Bs-dap_avg-signal52.180603
Spike_AFFX-r2-Bs-dap_3-5-ratio3.516459
Spike_AFFX-r2-Ec-bioB_5_signal64.620468
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.341558
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-19_Ler_MeJA_1h_Rep3_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-19_Ler_MeJA_1h_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-19_Ler_MeJA_1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 ;mol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample has been treated with 30 μM MeJA for 1h (This is the third of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.382921
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.966126
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.847229
Spike_AFFX-r2-Bs-dap_5_signal29.239830
NoiseAvg:3.52,Std:0.14,Min:3.2,Max:4.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.856581
#P15123
Spike_AFFX-r2-Bs-phe_M_signal14.839006
Corner-Avg:11468,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal53.952240
Spike_AFFX-r2-Ec-bioB_3_signal43.504761
Spike_AFFX-r2-Bs-lys_M_signal5.916342
Spike_AFFX-r2-P1-cre_3_signal2026.147827
Spike_AFFX-r2-Bs-lys_3-5-ratio1.942740
Spike_AFFX-r2-Bs-dap_M_signal71.577988
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.106117
Spike_AFFX-r2-Ec-bioB_avg-signal49.602146
Spike_AFFX-r2-Bs-thr_avg-signal24.270142
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal356.285858
Spike_AFFX-r2-Bs-phe_5_signal18.139479
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal755.143433
RawQ3.037124
Spike_AFFX-r2-Bs-lys_5_signal9.103121
Signal(A)3.809143
%A31.766769
Signal(All)139.763565
Corner+Avg:180,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal171.176285
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.815962
Spike_AFFX-r2-Ec-bioD_avg-signal555.714661
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.299866
Spike_AFFX-r2-Bs-lys_avg-signal10.901488
Spike_AFFX-r2-P1-cre_avg-signal2061.667480
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.933363
Spike_AFFX-r2-Bs-thr_3_signal36.366154
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.264816
Spike_AFFX-r2-Bs-dap_3_signal97.278564
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.119488
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal146.716858
#M441
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal17.685001
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.166712
Spike_AFFX-r2-Bs-thr_M_signal27.587687
Signal(P)208.573502
Spike_AFFX-r2-Bs-phe_3-5-ratio1.202679
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10010,Count:9
Spike_AFFX-r2-P1-cre_5_signal2097.187012
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7246
Signal(M)13.942899
BackgroundAvg:75.52,Std:1.00,Min:73.4,Max:78.0
Spike_AFFX-r2-Ec-bioC_avg-signal158.946564
Spike_AFFX-r2-Bs-dap_avg-signal66.032127
Spike_AFFX-r2-Bs-dap_3-5-ratio3.326920
Spike_AFFX-r2-Ec-bioB_5_signal51.349442
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.382921
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-20_athb1-2_MeJA_1h_Rep3_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-20_athb1-2_MeJA_1h_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-20_athb1-2_MeJA_1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: athb1-2
Stock Code:
Genetic Background: Ler-0
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: Transposon knock out mutation in AT3g01470
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample has been treated with 30 μM MeJA for 1h (This is the third of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.440652
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.977583
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.333062
Spike_AFFX-r2-Bs-dap_5_signal19.762236
NoiseAvg:2.95,Std:0.14,Min:2.6,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.046974
#P14958
Spike_AFFX-r2-Bs-phe_M_signal18.219982
Corner-Avg:10011,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal61.786343
Spike_AFFX-r2-Ec-bioB_3_signal63.652100
Spike_AFFX-r2-Bs-lys_M_signal6.334198
Spike_AFFX-r2-P1-cre_3_signal2650.576660
Spike_AFFX-r2-Bs-lys_3-5-ratio1.756355
Spike_AFFX-r2-Bs-dap_M_signal72.543564
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.543214
Spike_AFFX-r2-Ec-bioB_avg-signal57.729084
Spike_AFFX-r2-Bs-thr_avg-signal27.426237
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal422.527802
Spike_AFFX-r2-Bs-phe_5_signal21.991177
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal834.157593
RawQ2.668872
Spike_AFFX-r2-Bs-lys_5_signal9.591469
Signal(A)3.761004
%A32.428761
Signal(All)144.070206
Corner+Avg:155,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal154.476059
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal23.594328
Spike_AFFX-r2-Ec-bioD_avg-signal628.342712
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.576500
Spike_AFFX-r2-Bs-lys_avg-signal10.923897
Spike_AFFX-r2-P1-cre_avg-signal2680.967041
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.994739
Spike_AFFX-r2-Bs-thr_3_signal35.598579
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal21.268496
Spike_AFFX-r2-Bs-dap_3_signal94.920578
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.974208
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal162.781006
#M455
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal16.846024
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.948981
Spike_AFFX-r2-Bs-thr_M_signal36.633156
Signal(P)217.409439
Spike_AFFX-r2-Bs-phe_3-5-ratio1.072900
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8054,Count:9
Spike_AFFX-r2-P1-cre_5_signal2711.357422
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7397
Signal(M)14.089367
BackgroundAvg:63.48,Std:0.90,Min:61.7,Max:66.1
Spike_AFFX-r2-Ec-bioC_avg-signal158.628540
Spike_AFFX-r2-Bs-dap_avg-signal62.408794
Spike_AFFX-r2-Bs-dap_3-5-ratio4.803130
Spike_AFFX-r2-Ec-bioB_5_signal47.748806
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.440652
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-21_Ler_EtOH_4h_Rep1_Rep3_ATH1

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-21_Ler_EtOH_4h_Rep1_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-21_Ler_EtOH_4h_Rep1_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample is the control: mock treatment for 4h (This is the third of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.290102
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.353338
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.123548
Spike_AFFX-r2-Bs-dap_5_signal39.873775
NoiseAvg:2.88,Std:0.12,Min:2.6,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal13.153345
#P16092
Spike_AFFX-r2-Bs-phe_M_signal17.600206
Corner-Avg:11124,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal63.230946
Spike_AFFX-r2-Ec-bioB_3_signal55.445702
Spike_AFFX-r2-Bs-lys_M_signal8.884016
Spike_AFFX-r2-P1-cre_3_signal3174.303223
Spike_AFFX-r2-Bs-lys_3-5-ratio2.507717
Spike_AFFX-r2-Bs-dap_M_signal110.552788
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.783607
Spike_AFFX-r2-Ec-bioB_avg-signal56.008472
Spike_AFFX-r2-Bs-thr_avg-signal28.921469
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal523.277100
Spike_AFFX-r2-Bs-phe_5_signal16.960363
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal822.471497
RawQ2.465217
Spike_AFFX-r2-Bs-lys_5_signal10.485421
Signal(A)2.163410
%A28.101709
Signal(All)137.530991
Corner+Avg:172,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal184.778473
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.981531
Spike_AFFX-r2-Ec-bioD_avg-signal672.874268
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.548004
Spike_AFFX-r2-Bs-lys_avg-signal15.221301
Spike_AFFX-r2-P1-cre_avg-signal2759.919434
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.350285
Spike_AFFX-r2-Bs-thr_3_signal36.613739
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal19.180700
Spike_AFFX-r2-Bs-dap_3_signal124.954979
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.571770
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal190.140640
#M308
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.294468
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.971799
Spike_AFFX-r2-Bs-thr_M_signal36.997322
Signal(P)193.898880
Spike_AFFX-r2-Bs-phe_3-5-ratio1.355014
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8413,Count:9
Spike_AFFX-r2-P1-cre_5_signal2345.535645
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6410
Signal(M)9.719219
BackgroundAvg:61.94,Std:0.52,Min:60.7,Max:63.6
Spike_AFFX-r2-Ec-bioC_avg-signal187.459564
Spike_AFFX-r2-Bs-dap_avg-signal91.793846
Spike_AFFX-r2-Bs-dap_3-5-ratio3.133763
Spike_AFFX-r2-Ec-bioB_5_signal49.348778
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.290102
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-22_athb1-2_EtOH_4h_Rep3_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-22_athb1-2_EtOH_4h_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-22_athb1-2_EtOH_4h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: athb1-2
Stock Code:
Genetic Background: Ler-0
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: Transposon knock out mutation in AT3g01470
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample is the control: mock treatment for 4h (This is the third of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.375981
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.352676
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.043444
Spike_AFFX-r2-Bs-dap_5_signal18.728237
NoiseAvg:3.01,Std:0.12,Min:2.7,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal14.084645
#P15389
Spike_AFFX-r2-Bs-phe_M_signal18.484171
Corner-Avg:8173,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal57.025757
Spike_AFFX-r2-Ec-bioB_3_signal49.796181
Spike_AFFX-r2-Bs-lys_M_signal5.280385
Spike_AFFX-r2-P1-cre_3_signal3136.237061
Spike_AFFX-r2-Bs-lys_3-5-ratio1.696083
Spike_AFFX-r2-Bs-dap_M_signal73.804474
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.930116
Spike_AFFX-r2-Ec-bioB_avg-signal51.514954
Spike_AFFX-r2-Bs-thr_avg-signal29.852556
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal389.736206
Spike_AFFX-r2-Bs-phe_5_signal19.425373
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal705.138489
RawQ2.694570
Spike_AFFX-r2-Bs-lys_5_signal13.590681
Signal(A)3.161967
%A30.859272
Signal(All)142.442856
Corner+Avg:129,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal185.980133
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal20.479174
Spike_AFFX-r2-Ec-bioD_avg-signal547.437378
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.466026
Spike_AFFX-r2-Bs-lys_avg-signal13.973996
Spike_AFFX-r2-P1-cre_avg-signal2727.389648
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.674704
Spike_AFFX-r2-Bs-thr_3_signal41.269642
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal19.462906
Spike_AFFX-r2-Bs-dap_3_signal84.769936
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.809271
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal180.594498
#M382
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.050926
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.029822
Spike_AFFX-r2-Bs-thr_M_signal34.203377
Signal(P)209.356522
Spike_AFFX-r2-Bs-phe_3-5-ratio1.054249
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6485,Count:9
Spike_AFFX-r2-P1-cre_5_signal2318.542236
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7039
Signal(M)13.290870
BackgroundAvg:66.80,Std:0.82,Min:64.5,Max:68.9
Spike_AFFX-r2-Ec-bioC_avg-signal183.287323
Spike_AFFX-r2-Bs-dap_avg-signal59.100880
Spike_AFFX-r2-Bs-dap_3-5-ratio4.526317
Spike_AFFX-r2-Ec-bioB_5_signal47.722923
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.375981
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-23_Ler_MeJA_4h_Rep3_ATH1

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-23_Ler_MeJA_4h_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-23_Ler_MeJA_4h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a 120 μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample has been treated with 30 μM MeJA for 4h (This is the third of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.400608
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.359765
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.011044
Spike_AFFX-r2-Bs-dap_5_signal31.076828
NoiseAvg:3.23,Std:0.13,Min:2.9,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal13.870181
#P15295
Spike_AFFX-r2-Bs-phe_M_signal17.216818
Corner-Avg:11338,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal62.229755
Spike_AFFX-r2-Ec-bioB_3_signal40.328739
Spike_AFFX-r2-Bs-lys_M_signal8.116516
Spike_AFFX-r2-P1-cre_3_signal2616.927246
Spike_AFFX-r2-Bs-lys_3-5-ratio1.193233
Spike_AFFX-r2-Bs-dap_M_signal85.631752
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.541102
Spike_AFFX-r2-Ec-bioB_avg-signal47.482239
Spike_AFFX-r2-Bs-thr_avg-signal27.103285
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal367.822906
Spike_AFFX-r2-Bs-phe_5_signal17.833982
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal674.649963
RawQ2.833639
Spike_AFFX-r2-Bs-lys_5_signal14.022830
Signal(A)3.317811
%A31.310829
Signal(All)140.077835
Corner+Avg:180,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal152.589706
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal24.182547
Spike_AFFX-r2-Ec-bioD_avg-signal521.236450
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.053925
Spike_AFFX-r2-Bs-lys_avg-signal12.957284
Spike_AFFX-r2-P1-cre_avg-signal2270.735352
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.635248
Spike_AFFX-r2-Bs-thr_3_signal35.245541
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal19.744448
Spike_AFFX-r2-Bs-dap_3_signal119.225426
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.834171
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal133.265732
#M373
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal16.732508
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.145003
Spike_AFFX-r2-Bs-thr_M_signal32.194134
Signal(P)207.052948
Spike_AFFX-r2-Bs-phe_3-5-ratio1.355981
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9293,Count:9
Spike_AFFX-r2-P1-cre_5_signal1924.543701
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7142
Signal(M)12.345412
BackgroundAvg:71.14,Std:0.82,Min:69.4,Max:73.4
Spike_AFFX-r2-Ec-bioC_avg-signal142.927719
Spike_AFFX-r2-Bs-dap_avg-signal78.644669
Spike_AFFX-r2-Bs-dap_3-5-ratio3.836473
Spike_AFFX-r2-Ec-bioB_5_signal39.888214
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.400608
NF1.000000
HZ4
Tau0.015000

Slide: Baima_572-24_athb1-2_MeJA_4h_Rep3_ATH1

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Baima_572-24_athb1-2_MeJA_4h_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Baima_572-24_athb1-2_MeJA_4h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: athb1-2
Stock Code:
Genetic Background: Ler-0
Age: 7 dag
Growth Conditions:
StratificationArabidopsis seeds were sowed on a nylon mesh in plates containing a synthetic medium and then cold treated for 3 - 4 days at 4 °C in the dark to synchronise germination.
SterilisationSeeds were surface sterilized for 10 min in 30% (v/v) commercial bleach and 0.02% Triton X-100, rinsed three times with sterile distilled water and dried in a laminar flow hood.
ProtocolArabidopsis plants were germinated on a nylon mesh in plates containing solid MS medium and closed with 3MM Micropore tape. Plants were grown for 7 days in growth chambers at 21 °C, under continuous light condition and a μmol sec-1 light intensity.
Substrate Sterilising ProcedureMS medium and the nylon meshes were sterilised in autoclave for 12 and 20 minutes respectively.
Plant Spacing36 plants per plate
Temperature21 °C average, 21 °C day, 21 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: Murashige and Skoog salts (pH 5.8) 4,3 gr/l Sucrose 1% Agar 0.8% Inositol 100 mg/l MES 0,5% g/l Thiamine 1 mg/l Pyridoxine 0,5 mg/l Nicotinic acid 0,5 mg/l
Lighting(Source: Fluorescent manufactured by Philips Master TL-D 18W/840. Intensity: 120µEinsteins. Wavelength: White)Constant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: Transposon knock out mutation in AT3g01470
Tissue: whole plant
in vivo Treatment: Plants were treated with methyl jasmonate (MeJA) after 7 days of growth on a nylon mesh in plates. For the treatment, the nylon meshes with the seedlings were transferred on fresh solid MS medium to which equal volumes of a MeJA stock (dissolved in ethanol, final concentration 30 μM; Duchefa) or ethanol (mock) had been added. After 1 h and 4 h of incubation the plants were collected and immediately frozen in liquid nitrogen for total RNA extraction. This sample has been treated with 30 μM MeJA for 4h (This is the third of three experimental replicates).
Additional Organism Information:
Sample DescriptionPlants didn’t show any alteration after the treatment.
Other Information:
Timecourse start procedureStart time was the time when 7-days-old seedlings were transferred on MS medium containing MeJA or ethanol.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.326974
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.219033
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.140691
Spike_AFFX-r2-Bs-dap_5_signal11.269302
NoiseAvg:3.23,Std:0.11,Min:2.9,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.419711
#P15104
Spike_AFFX-r2-Bs-phe_M_signal19.603445
Corner-Avg:12011,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal69.553566
Spike_AFFX-r2-Ec-bioB_3_signal58.647491
Spike_AFFX-r2-Bs-lys_M_signal10.488930
Spike_AFFX-r2-P1-cre_3_signal3051.862061
Spike_AFFX-r2-Bs-lys_3-5-ratio3.441986
Spike_AFFX-r2-Bs-dap_M_signal74.513420
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.144672
Spike_AFFX-r2-Ec-bioB_avg-signal59.871685
Spike_AFFX-r2-Bs-thr_avg-signal23.168154
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal489.949219
Spike_AFFX-r2-Bs-phe_5_signal16.980192
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal928.819885
RawQ2.820048
Spike_AFFX-r2-Bs-lys_5_signal11.106018
Signal(A)3.160199
%A31.898291
Signal(All)142.440186
Corner+Avg:188,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal195.055084
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal26.955139
Spike_AFFX-r2-Ec-bioD_avg-signal709.384521
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.216568
Spike_AFFX-r2-Bs-lys_avg-signal19.940569
Spike_AFFX-r2-P1-cre_avg-signal2777.686523
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.885138
Spike_AFFX-r2-Bs-thr_3_signal38.171978
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal21.179594
Spike_AFFX-r2-Bs-dap_3_signal127.211418
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.895747
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal194.792496
#M430
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal38.226761
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.001348
Spike_AFFX-r2-Bs-thr_M_signal23.912777
Signal(P)213.237106
Spike_AFFX-r2-Bs-phe_3-5-ratio1.587446
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10017,Count:9
Spike_AFFX-r2-P1-cre_5_signal2503.510742
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7276
Signal(M)12.404114
BackgroundAvg:69.03,Std:0.54,Min:67.8,Max:70.4
Spike_AFFX-r2-Ec-bioC_avg-signal194.923798
Spike_AFFX-r2-Bs-dap_avg-signal70.998047
Spike_AFFX-r2-Bs-dap_3-5-ratio11.288314
Spike_AFFX-r2-Ec-bioB_5_signal51.414001
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.326974
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team