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Experiment: Effect of jasmonate of gene expression in the mutants jin1 and jut

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-634

The jasmonate signal pathway regulates plant growth, plant growth in response to the environment, and responses to pests and pathogens. Its activation is associated with transcriptional re-profiling of as much as 10% of the genome. One transcription factor that regulates JA responses in JIN1/MYC2. We discovered another potentially important regulator of JA responses which we have named JUT. Here we examine gene expression induced by jasmonte in wild type, jin1-1, jut, and in the double mutant jin1-1/jut.

About the Experimenter

Name: John Turner
Head of Lab Name: John Turner
Lab:
Address:School of Biological Sciences, University of East Anglia
Norwich, Norfolk, NR4 7TJ, UNITED KINGDOM
Postcode:
Country:
 
Telephone Number: 01603 592192
Fax Number: 01603 592250

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; strain_or_line_design;genetic_modification_design
Number of Slides:8
 
Experimental Parameters:
parametercompound_based_treatment
parametergene_knock_out
parameterinduced_mutation
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Turner: Effect of jasmonate of gene expression in the mutants jin1 and jut

Slide: Turner_634-8_jin1-1-jut-MeJA_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 ("Turner_634-8_jin1-1-jut-MeJA_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: Turner_634-8_jin1-1-jut-MeJA_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: jin1-1-jut
Stock Code:
Genetic Background: Col-0
Age: 1.02
Growth Conditions:
StratificationIn sterile water at 4 degrees centrigade for 48 hours
SterilisationWash ethanol 5 mins; wash SDW 5 mins; 20% household bleach 15 mins; wash SDW 5 mins; repeat SDW wash further 2 times
ProtocolPlants were raised in anexic conditions in MS media at 16 h day, 70-90 micromoles per square metre per second. Plates were held vertically and seeds were sown in a horizontal line. Twelve-day-old seedllings were transferred to MS solid media containing 20 uM MeJA, and after 30 mins seedlings were snap-frozen in eppendorf tubes immersed in LN2
Percentage Agrose0.7%
Substrate Sterilising ProcedureAutoclave, 15 psi, 15 mins
Plant Spacing0.5 cm
Temperature22 °C average, 22 °C day, 22 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: 0.5% sucrose, and 0.5% sucrose with methyl jasmonate, 20 micromolar
Lighting(Source: Cool white fluorescent manufactured by SANYO. Intensity: 70-90µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: T-DNA knock out mutation in At2g46510
Tissue: whole plant
Additional Organism Information:
Sample DescriptionSeedlings were 12 days old when harvested
Other Information:

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:0.691467
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-ratio1.325495
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.680630
Spike_AFFX-r2-Bs-dap_5_signal116.592590
NoiseAvg:2.99,Std:0.10,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_signal37.831329
#P14903
Spike_AFFX-r2-Bs-phe_M_signal55.756332
Corner-Avg:16472,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal93.418472
Spike_AFFX-r2-Ec-bioB_3_signal96.963722
Spike_AFFX-r2-Bs-lys_M_signal28.514563
Spike_AFFX-r2-P1-cre_3_signal4447.844238
Spike_AFFX-r2-Bs-lys_3-5-ratio1.464298
Spike_AFFX-r2-Bs-dap_M_signal291.679626
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.731256
Spike_AFFX-r2-Ec-bioB_avg-signal82.692352
Spike_AFFX-r2-Bs-thr_avg-signal101.641472
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal902.245300
Spike_AFFX-r2-Bs-phe_5_signal46.377033
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1188.611816
RawQ2.640557
Spike_AFFX-r2-Bs-lys_5_signal29.136396
Signal(A)4.736432
%A32.836475
Signal(All)143.151306
Corner+Avg:129,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal222.289337
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal65.464447
Spike_AFFX-r2-Ec-bioD_avg-signal1045.428589
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.335381
Spike_AFFX-r2-Bs-lys_avg-signal33.438442
Spike_AFFX-r2-P1-cre_avg-signal3901.727051
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.828146
Spike_AFFX-r2-Bs-thr_3_signal178.989716
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-signal55.865936
Spike_AFFX-r2-Bs-dap_3_signal359.834045
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.317393
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal229.599609
#M417
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal42.664364
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.968161
Spike_AFFX-r2-Bs-thr_M_signal88.103363
Signal(P)216.256714
Spike_AFFX-r2-Bs-phe_3-5-ratio1.411570
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15457,Count:9
Spike_AFFX-r2-P1-cre_5_signal3355.609619
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7490
Signal(M)16.622925
BackgroundAvg:70.19,Std:0.51,Min:69.0,Max:71.5
Spike_AFFX-r2-Ec-bioC_avg-signal225.944473
Spike_AFFX-r2-Bs-dap_avg-signal256.035431
Spike_AFFX-r2-Bs-dap_3-5-ratio3.086251
Spike_AFFX-r2-Ec-bioB_5_signal57.694851
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.691467
NF1.000000
HZ4
Tau0.015000

Slide: Turner_634-7_jin1-1-jut-mock_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 ("Turner_634-7_jin1-1-jut-mock_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: Turner_634-7_jin1-1-jut-mock_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: jin1-1-jut
Stock Code:
Genetic Background: Col-0
Age: 1.02
Growth Conditions:
StratificationIn sterile water at 4 degrees centrigade for 48 hours
SterilisationWash ethanol 5 mins; wash SDW 5 mins; 20% household bleach 15 mins; wash SDW 5 mins; repeat SDW wash further 2 times
ProtocolPlants were raised in anexic conditions in MS media at 16 h day, 70-90 micromoles per square metre per second. Plates were held vertically and seeds were sown in a horizontal line. After 12 days seedlings were snap-frozen in eppendorf tubes immersed in LN2
Percentage Agrose0.7%
Substrate Sterilising ProcedureAutoclave, 15 psi, 15 mins
Plant Spacing0.5 cm
Temperature22 °C average, 22 °C day, 22 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: 0.5% sucrose,
Lighting(Source: Cool white fluorescent manufactured by SANYO. Intensity: 70-90µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: T-DNA knock out mutation in At2g46510
Tissue: whole plant
Additional Organism Information:
Sample DescriptionSeedlings were 12 days old when harvested
Other Information:

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:0.776642
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-ratio1.220252
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.393617
Spike_AFFX-r2-Bs-dap_5_signal114.251091
NoiseAvg:2.63,Std:0.07,Min:2.4,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal34.821449
#P14905
Spike_AFFX-r2-Bs-phe_M_signal81.797035
Corner-Avg:17722,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal122.894173
Spike_AFFX-r2-Ec-bioB_3_signal115.188095
Spike_AFFX-r2-Bs-lys_M_signal39.387146
Spike_AFFX-r2-P1-cre_3_signal5679.564453
Spike_AFFX-r2-Bs-lys_3-5-ratio1.824177
Spike_AFFX-r2-Bs-dap_M_signal291.751678
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.834630
Spike_AFFX-r2-Ec-bioB_avg-signal106.912102
Spike_AFFX-r2-Bs-thr_avg-signal142.345551
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1141.408447
Spike_AFFX-r2-Bs-phe_5_signal63.041454
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1648.444824
RawQ2.498740
Spike_AFFX-r2-Bs-lys_5_signal33.725388
Signal(A)5.002564
%A32.858395
Signal(All)146.983948
Corner+Avg:126,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal331.989014
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal134.151581
Spike_AFFX-r2-Ec-bioD_avg-signal1394.926636
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.344147
Spike_AFFX-r2-Bs-lys_avg-signal44.877869
Spike_AFFX-r2-P1-cre_avg-signal5166.992188
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_signal272.813171
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-signal92.996681
Spike_AFFX-r2-Bs-dap_3_signal502.566803
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.444220
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal304.512970
#M410
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal61.521072
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.090230
Spike_AFFX-r2-Bs-thr_M_signal119.402054
Signal(P)221.917480
Spike_AFFX-r2-Bs-phe_3-5-ratio2.127990
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16402,Count:9
Spike_AFFX-r2-P1-cre_5_signal4654.419922
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7495
Signal(M)18.365007
BackgroundAvg:63.74,Std:0.48,Min:61.9,Max:64.7
Spike_AFFX-r2-Ec-bioC_avg-signal318.250977
Spike_AFFX-r2-Bs-dap_avg-signal302.856537
Spike_AFFX-r2-Bs-dap_3-5-ratio4.398792
Spike_AFFX-r2-Ec-bioB_5_signal82.654030
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.776642
NF1.000000
HZ4
Tau0.015000

Slide: Turner_634-6_jut-MeJA_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 ("Turner_634-6_jut-MeJA_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: Turner_634-6_jut-MeJA_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: jut
Stock Code:
Genetic Background: Col-0
Age: 1.02
Growth Conditions:
StratificationIn sterile water at 4 degrees centrigade for 48 hours
SterilisationWash ethanol 5 mins; wash SDW 5 mins; 20% household bleach 15 mins; wash SDW 5 mins; repeat SDW wash further 2 times
ProtocolPlants were raised in anexic conditions in MS media at 16 h day, 70-90 micromoles per square metre per second. Plates were held vertically and seeds were sown in a horizontal line. Twelve-day-old seedllings were transferred to MS solid media containing 20 uM MeJA, and after 30 mins seedlings were snap-frozen in eppendorf tubes immersed in LN2
Percentage Agrose0.7%
Substrate Sterilising ProcedureAutoclave, 15 psi, 15 mins
Plant Spacing0.5 cm
Temperature22 °C average, 22 °C day, 22 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: 0.5% sucrose, and 0.5% sucrose with methyl jasmonate, 20 micromolar
Lighting(Source: Cool white fluorescent manufactured by SANYO. Intensity: 70-90µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: T-DNA knock out mutation in At2g46510
Tissue: whole plant
Additional Organism Information:
Sample DescriptionSeedlings were 12 days old when harvested
Other Information:

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:0.873827
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-ratio1.047883
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.651641
Spike_AFFX-r2-Bs-dap_5_signal42.217403
NoiseAvg:2.54,Std:0.08,Min:2.3,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_signal17.636127
#P14743
Spike_AFFX-r2-Bs-phe_M_signal62.840851
Corner-Avg:16342,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal119.979111
Spike_AFFX-r2-Ec-bioB_3_signal107.229477
Spike_AFFX-r2-Bs-lys_M_signal39.228683
Spike_AFFX-r2-P1-cre_3_signal4891.626953
Spike_AFFX-r2-Bs-lys_3-5-ratio2.223879
Spike_AFFX-r2-Bs-dap_M_signal224.751083
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.089352
Spike_AFFX-r2-Ec-bioB_avg-signal97.377197
Spike_AFFX-r2-Bs-thr_avg-signal94.387993
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1107.381714
Spike_AFFX-r2-Bs-phe_5_signal50.928169
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1565.585571
RawQ2.502965
Spike_AFFX-r2-Bs-lys_5_signal24.031460
Signal(A)4.890775
%A33.476547
Signal(All)145.489609
Corner+Avg:117,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal320.565460
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal80.601143
Spike_AFFX-r2-Ec-bioD_avg-signal1336.483643
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.633934
Spike_AFFX-r2-Bs-lys_avg-signal38.901066
Spike_AFFX-r2-P1-cre_avg-signal4779.866211
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.889522
Spike_AFFX-r2-Bs-thr_3_signal177.937088
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-signal64.790047
Spike_AFFX-r2-Bs-dap_3_signal339.998291
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.413772
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal251.163589
#M431
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal53.443054
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.276321
Spike_AFFX-r2-Bs-thr_M_signal87.590729
Signal(P)222.050018
Spike_AFFX-r2-Bs-phe_3-5-ratio1.582644
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16002,Count:9
Spike_AFFX-r2-P1-cre_5_signal4668.105469
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7636
Signal(M)17.607122
BackgroundAvg:62.98,Std:0.70,Min:61.1,Max:64.6
Spike_AFFX-r2-Ec-bioC_avg-signal285.864532
Spike_AFFX-r2-Bs-dap_avg-signal202.322266
Spike_AFFX-r2-Bs-dap_3-5-ratio8.053511
Spike_AFFX-r2-Ec-bioB_5_signal64.923012
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.873827
NF1.000000
HZ4
Tau0.015000

Slide: Turner_634-5_jut-mock_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 ("Turner_634-5_jut-mock_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: Turner_634-5_jut-mock_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: jut
Stock Code:
Genetic Background: Col-0
Age: 1.02
Growth Conditions:
StratificationIn sterile water at 4 degrees centrigade for 48 hours
SterilisationWash ethanol 5 mins; wash SDW 5 mins; 20% household bleach 15 mins; wash SDW 5 mins; repeat SDW wash further 2 times
ProtocolPlants were raised in anexic conditions in MS media at 16 h day, 70-90 micromoles per square metre per second. Plates were held vertically and seeds were sown in a horizontal line. After 12 days seedlings were snap-frozen in eppendorf tubes immersed in LN2
Percentage Agrose0.7%
Substrate Sterilising ProcedureAutoclave, 15 psi, 15 mins
Plant Spacing0.5 cm
Temperature22 °C average, 22 °C day, 22 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: 0.5% sucrose,
Lighting(Source: Cool white fluorescent manufactured by SANYO. Intensity: 70-90µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: T-DNA knock out mutation in At2g46510
Tissue: whole plant
Additional Organism Information:
Sample DescriptionSeedlings were 12 days old when harvested
Other Information:

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:0.627502
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-ratio1.230760
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.297098
Spike_AFFX-r2-Bs-dap_5_signal76.738525
NoiseAvg:2.91,Std:0.10,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_signal21.435242
#P15122
Spike_AFFX-r2-Bs-phe_M_signal51.594803
Corner-Avg:16072,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal104.185463
Spike_AFFX-r2-Ec-bioB_3_signal69.953537
Spike_AFFX-r2-Bs-lys_M_signal25.427267
Spike_AFFX-r2-P1-cre_3_signal4157.885254
Spike_AFFX-r2-Bs-lys_3-5-ratio1.479925
Spike_AFFX-r2-Bs-dap_M_signal245.905380
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.071402
Spike_AFFX-r2-Ec-bioB_avg-signal76.023262
Spike_AFFX-r2-Bs-thr_avg-signal99.367317
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal755.766296
Spike_AFFX-r2-Bs-phe_5_signal35.841656
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1222.034912
RawQ2.650751
Spike_AFFX-r2-Bs-lys_5_signal27.553070
Signal(A)4.541418
%A31.990355
Signal(All)141.538742
Corner+Avg:120,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal237.367874
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal84.946899
Spike_AFFX-r2-Ec-bioD_avg-signal988.900635
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.295486
Spike_AFFX-r2-Bs-lys_avg-signal31.252268
Spike_AFFX-r2-P1-cre_avg-signal3768.096680
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.714160
Spike_AFFX-r2-Bs-thr_3_signal194.447693
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-signal57.461121
Spike_AFFX-r2-Bs-dap_3_signal300.385651
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.616948
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal204.028336
#M391
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal40.776466
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.163406
Spike_AFFX-r2-Bs-thr_M_signal82.219025
Signal(P)210.879120
Spike_AFFX-r2-Bs-phe_3-5-ratio2.370061
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15806,Count:9
Spike_AFFX-r2-P1-cre_5_signal3378.307861
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7297
Signal(M)16.486113
BackgroundAvg:70.85,Std:0.82,Min:68.9,Max:72.7
Spike_AFFX-r2-Ec-bioC_avg-signal220.698105
Spike_AFFX-r2-Bs-dap_avg-signal207.676514
Spike_AFFX-r2-Bs-dap_3-5-ratio3.914405
Spike_AFFX-r2-Ec-bioB_5_signal53.930786
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.627502
NF1.000000
HZ4
Tau0.015000

Slide: Turner_634-4_jin1-1-MeJA_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 ("Turner_634-4_jin1-1-MeJA_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: Turner_634-4_jin1-1-MeJA_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: jin1-1
Stock Code:
Genetic Background: Col-0
Age: 1.02
Growth Conditions:
StratificationIn sterile water at 4 degrees centrigade for 48 hours
SterilisationWash ethanol 5 mins; wash SDW 5 mins; 20% household bleach 15 mins; wash SDW 5 mins; repeat SDW wash further 2 times
ProtocolPlants were raised in anexic conditions in MS media at 16 h day, 70-90 micromoles per square metre per second. Plates were held vertically and seeds were sown in a horizontal line. After 12 days seedlings were snap-frozen in eppendorf tubes immersed in LN2
Percentage Agrose0.7%
Substrate Sterilising ProcedureAutoclave, 15 psi, 15 mins
Plant Spacing0.5 cm
Temperature22 °C average, 22 °C day, 22 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: 0.5% sucrose,
Lighting(Source: Cool white fluorescent manufactured by SANYO. Intensity: 70-90µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: T-DNA induced mutation in At1g32640
Tissue: whole plant
Additional Organism Information:
Sample DescriptionSeedlings were 12 days old when harvested
Other Information:

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:0.796894
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-ratio1.266745
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.749590
Spike_AFFX-r2-Bs-dap_5_signal85.473404
NoiseAvg:2.75,Std:0.10,Min:2.4,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_signal33.439499
#P14556
Spike_AFFX-r2-Bs-phe_M_signal52.031937
Corner-Avg:16763,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal105.783333
Spike_AFFX-r2-Ec-bioB_3_signal112.919807
Spike_AFFX-r2-Bs-lys_M_signal17.159176
Spike_AFFX-r2-P1-cre_3_signal5456.893555
Spike_AFFX-r2-Bs-lys_3-5-ratio1.465269
Spike_AFFX-r2-Bs-dap_M_signal247.963058
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.995989
Spike_AFFX-r2-Ec-bioB_avg-signal94.414619
Spike_AFFX-r2-Bs-thr_avg-signal94.219460
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1011.744934
Spike_AFFX-r2-Bs-phe_5_signal36.330692
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1578.692627
RawQ2.554430
Spike_AFFX-r2-Bs-lys_5_signal30.600779
Signal(A)4.965870
%A34.366505
Signal(All)149.281403
Corner+Avg:125,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal292.478821
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal88.319885
Spike_AFFX-r2-Ec-bioD_avg-signal1295.218750
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.814117
Spike_AFFX-r2-Bs-lys_avg-signal30.866110
Spike_AFFX-r2-P1-cre_avg-signal4882.349609
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.819377
Spike_AFFX-r2-Bs-thr_3_signal167.063370
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-signal58.894169
Spike_AFFX-r2-Bs-dap_3_signal321.427826
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.560366
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal270.444794
#M415
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal44.838371
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.081473
Spike_AFFX-r2-Bs-thr_M_signal82.155533
Signal(P)230.743210
Spike_AFFX-r2-Bs-phe_3-5-ratio2.430999
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15949,Count:9
Spike_AFFX-r2-P1-cre_5_signal4307.806152
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7839
Signal(M)18.031166
BackgroundAvg:70.19,Std:1.05,Min:67.3,Max:72.4
Spike_AFFX-r2-Ec-bioC_avg-signal281.461792
Spike_AFFX-r2-Bs-dap_avg-signal218.288086
Spike_AFFX-r2-Bs-dap_3-5-ratio3.760560
Spike_AFFX-r2-Ec-bioB_5_signal64.540726
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.796894
NF1.000000
HZ4
Tau0.015000

Slide: Turner_634-3_jin1-1- mock_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 ("Turner_634-3_jin1-1- mock_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: Turner_634-3_jin1-1- mock_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: jin1-1
Stock Code:
Genetic Background: Col-0
Age: 1.02
Growth Conditions:
StratificationIn sterile water at 4 degrees centrigade for 48 hours
SterilisationWash ethanol 5 mins; wash SDW 5 mins; 20% household bleach 15 mins; wash SDW 5 mins; repeat SDW wash further 2 times
ProtocolPlants were raised in anexic conditions in MS media at 16 h day, 70-90 micromoles per square metre per second. Plates were held vertically and seeds were sown in a horizontal line. After 12 days seedlings were snap-frozen in eppendorf tubes immersed in LN2
Percentage Agrose0.7%
Substrate Sterilising ProcedureAutoclave, 15 psi, 15 mins
Plant Spacing0.5 cm
Temperature22 °C average, 22 °C day, 22 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: 0.5% sucrose,
Lighting(Source: Cool white fluorescent manufactured by SANYO. Intensity: 70-90µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: T-DNA induced mutation in At1g32640
Tissue: whole plant
Additional Organism Information:
Sample DescriptionSeedlings were 12 days old when harvested
Other Information:

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:0.61096
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-ratio1.336695
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.672906
Spike_AFFX-r2-Bs-dap_5_signal75.525085
NoiseAvg:2.90,Std:0.08,Min:2.8,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_signal24.607086
#P15265
Spike_AFFX-r2-Bs-phe_M_signal52.436634
Corner-Avg:17323,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal107.390518
Spike_AFFX-r2-Ec-bioB_3_signal100.213478
Spike_AFFX-r2-Bs-lys_M_signal28.057077
Spike_AFFX-r2-P1-cre_3_signal4631.581543
Spike_AFFX-r2-Bs-lys_3-5-ratio2.326881
Spike_AFFX-r2-Bs-dap_M_signal242.088989
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.275864
Spike_AFFX-r2-Ec-bioB_avg-signal89.169281
Spike_AFFX-r2-Bs-thr_avg-signal95.850777
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal938.272034
Spike_AFFX-r2-Bs-phe_5_signal48.460037
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1364.321777
RawQ2.576690
Spike_AFFX-r2-Bs-lys_5_signal24.917614
Signal(A)4.096354
%A31.411661
Signal(All)143.264023
Corner+Avg:151,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal255.239304
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal97.456390
Spike_AFFX-r2-Ec-bioD_avg-signal1151.296875
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.922401
Spike_AFFX-r2-Bs-lys_avg-signal36.985001
Spike_AFFX-r2-P1-cre_avg-signal4048.265381
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_signal179.037811
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-signal66.117683
Spike_AFFX-r2-Bs-dap_3_signal363.315338
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.454079
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal265.007568
#M380
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal57.980312
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.963140
Spike_AFFX-r2-Bs-thr_M_signal83.907433
Signal(P)211.774063
Spike_AFFX-r2-Bs-phe_3-5-ratio2.011067
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16164,Count:9
Spike_AFFX-r2-P1-cre_5_signal3464.949219
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7165
Signal(M)15.186950
BackgroundAvg:64.46,Std:0.53,Min:62.9,Max:66.0
Spike_AFFX-r2-Ec-bioC_avg-signal260.123444
Spike_AFFX-r2-Bs-dap_avg-signal226.976456
Spike_AFFX-r2-Bs-dap_3-5-ratio4.810525
Spike_AFFX-r2-Ec-bioB_5_signal59.903835
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.610960
NF1.000000
HZ4
Tau0.015000

Slide: Turner_634-2_Col0-MeJA_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 ("Turner_634-2_Col0-MeJA_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: Turner_634-2_Col0-MeJA_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 1.02
Growth Conditions:
StratificationIn sterile water at 4 degrees centrigade for 48 hours
SterilisationWash ethanol 5 mins; wash SDW 5 mins; 20% household bleach 15 mins; wash SDW 5 mins; repeat SDW wash further 2 times
ProtocolPlants were raised in anexic conditions in MS media at 16 h day, 70-90 micromoles per square metre per second. Plates were held vertically and seeds were sown in a horizontal line. Twelve-day-old seedllings were transferred to MS solid media containing 20 uM MeJA, and after 30 mins seedlings were snap-frozen in eppendorf tubes immersed in LN2
Percentage Agrose0.7%
Substrate Sterilising ProcedureAutoclave, 15 psi, 15 mins
Plant Spacing0.5 cm
Temperature22 °C average, 22 °C day, 22 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: 0.5% sucrose, and 0.5% sucrose with methyl jasmonate, 20 micromolar
Lighting(Source: Cool white fluorescent manufactured by SANYO. Intensity: 70-90µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
Additional Organism Information:
Sample DescriptionSeedlings were 12 days old when harvested
Other Information:
ecotype_habitatBerlin Arabidopsis scock centre

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:0.586354
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-ratio1.221399
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.724982
Spike_AFFX-r2-Bs-dap_5_signal179.269989
NoiseAvg:2.83,Std:0.09,Min:2.6,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_signal46.019226
#P15354
Spike_AFFX-r2-Bs-phe_M_signal90.339767
Corner-Avg:17821,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal92.007576
Spike_AFFX-r2-Ec-bioB_3_signal96.885925
Spike_AFFX-r2-Bs-lys_M_signal45.607845
Spike_AFFX-r2-P1-cre_3_signal4314.545410
Spike_AFFX-r2-Bs-lys_3-5-ratio1.805383
Spike_AFFX-r2-Bs-dap_M_signal418.129578
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.686675
Spike_AFFX-r2-Ec-bioB_avg-signal81.686615
Spike_AFFX-r2-Bs-thr_avg-signal167.723526
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal888.691284
Spike_AFFX-r2-Bs-phe_5_signal71.358910
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1207.327148
RawQ2.555001
Spike_AFFX-r2-Bs-lys_5_signal37.984413
Signal(A)3.687472
%A31.135468
Signal(All)139.627304
Corner+Avg:151,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal230.788010
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal149.084808
Spike_AFFX-r2-Ec-bioD_avg-signal1048.009277
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.312584
Spike_AFFX-r2-Bs-lys_avg-signal50.722900
Spike_AFFX-r2-P1-cre_avg-signal3923.504150
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.551951
Spike_AFFX-r2-Bs-thr_3_signal307.715607
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-signal103.594490
Spike_AFFX-r2-Bs-dap_3_signal615.094910
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.358545
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal223.889816
#M354
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal68.576431
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.030811
Spike_AFFX-r2-Bs-thr_M_signal149.435760
Signal(P)205.413528
Spike_AFFX-r2-Bs-phe_3-5-ratio2.089225
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15912,Count:9
Spike_AFFX-r2-P1-cre_5_signal3532.462891
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7102
Signal(M)13.534381
BackgroundAvg:62.93,Std:0.66,Min:61.6,Max:65.3
Spike_AFFX-r2-Ec-bioC_avg-signal227.338913
Spike_AFFX-r2-Bs-dap_avg-signal404.164825
Spike_AFFX-r2-Bs-dap_3-5-ratio3.431109
Spike_AFFX-r2-Ec-bioB_5_signal56.166351
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.586354
NF1.000000
HZ4
Tau0.015000

Slide: Turner_634-1_Col0-mock _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 ("Turner_634-1_Col0-mock _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: Turner_634-1_Col0-mock _Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Age: 1.02
Growth Conditions:
StratificationIn sterile water at 4 degrees centrigade for 48 hours
SterilisationWash ethanol 5 mins; wash SDW 5 mins; 20% household bleach 15 mins; wash SDW 5 mins; repeat SDW wash further 2 times
ProtocolPlants were raised in anexic conditions in MS media at 16 h day, 70-90 micromoles per square metre per second. Plates were held vertically and seeds were sown in a horizontal line.
Percentage Agrose0.7%
Substrate Sterilising ProcedureAutoclave, 15 psi, 15 mins
Plant Spacing0.5 cm
Temperature22 °C average, 22 °C day, 22 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture. Modifications: 0.5% sucrose
Lighting(Source: Cool white fluorescent manufactured by SANYO. Intensity: 70-90µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Tissue: whole plant
Additional Organism Information:
Sample DescriptionSeedlings were 12 days old when harvested
Other Information:
ecotype_habitatBerlin Arabidopsis scock centre

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:0.73289
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-ratio1.206786
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.884043
Spike_AFFX-r2-Bs-dap_5_signal138.558655
NoiseAvg:2.61,Std:0.08,Min:2.4,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal37.246738
#P15124
Spike_AFFX-r2-Bs-phe_M_signal56.497231
Corner-Avg:17084,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal130.952545
Spike_AFFX-r2-Ec-bioB_3_signal105.841545
Spike_AFFX-r2-Bs-lys_M_signal33.961464
Spike_AFFX-r2-P1-cre_3_signal4867.409180
Spike_AFFX-r2-Bs-lys_3-5-ratio1.639320
Spike_AFFX-r2-Bs-dap_M_signal354.782867
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.070849
Spike_AFFX-r2-Ec-bioB_avg-signal97.657326
Spike_AFFX-r2-Bs-thr_avg-signal123.222115
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal893.928711
Spike_AFFX-r2-Bs-phe_5_signal57.753136
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1586.850220
RawQ2.381369
Spike_AFFX-r2-Bs-lys_5_signal37.980980
Signal(A)4.564572
%A31.797457
Signal(All)142.645782
Corner+Avg:136,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal308.002228
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal122.678947
Spike_AFFX-r2-Ec-bioD_avg-signal1240.389404
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.304253
Spike_AFFX-r2-Bs-lys_avg-signal44.735138
Spike_AFFX-r2-P1-cre_avg-signal4450.387695
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.898290
Spike_AFFX-r2-Bs-thr_3_signal188.872604
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-signal78.976440
Spike_AFFX-r2-Bs-dap_3_signal466.574829
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.775142
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal292.209961
#M433
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal62.262978
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.054044
Spike_AFFX-r2-Bs-thr_M_signal143.546997
Signal(P)212.476196
Spike_AFFX-r2-Bs-phe_3-5-ratio2.124195
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15461,Count:9
Spike_AFFX-r2-P1-cre_5_signal4033.366455
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7253
Signal(M)16.520981
BackgroundAvg:57.77,Std:0.45,Min:56.6,Max:58.8
Spike_AFFX-r2-Ec-bioC_avg-signal300.106079
Spike_AFFX-r2-Bs-dap_avg-signal319.972107
Spike_AFFX-r2-Bs-dap_3-5-ratio3.367345
Spike_AFFX-r2-Ec-bioB_5_signal56.177872
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.732890
NF1.000000
HZ4
Tau0.015000


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