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Experiment: Identification of Genes Differentially Expressed in fry 2-1 Mutants

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-611

Low temperature, drought, and high salinity induce the expression of many plant genes. Recessive mutations in FIERY2 (FRY2) result in super-induction of the DRE/CRT class of stress-responsive genes, suggesting that FRY2 negatively regulates stress and ABA activation of these genes. The aim of this experiment is to identify genes differentially expressed in fry 2-1 mutant and their comparison with C24 wild type Arabidopsis plants. For this purpose, both C24 and fry2-1 mutant seeds were surface sterilized by 70% ethanol and washed with distilled water for several times. Seeds were grown on 1/4 strength Murashigee and Skoog basal media containing 0.5 % sucrose, solidified with 0.8 % plant cell tissue grade agar. Approximately 200 seeds were sown on each petri dish and stratified for 4 days at 4°C. Then, they were transferred to a growth chamber providing 16 h of light and 8 h of darkness at 25°C.After 10 days of growth at these conditions, total RNA was extracted from 100mg of seedlings by using TRIzol (Invitrogen, Cat No. 15596-018) method according to the manufacturer's procedure. Then, total RNA samples were treated with DNase I (Qiagen, Cat. No. 79254) at 37°C for 1 hours and cleaned using Qiagen minicolumns.

About the Experimenter

Name: EMRE AKSOY
Head of Lab Name:Dr. HISASHI KOIWA
Lab:
Address:Department of Horticultural Sciences
Texas A
&
M University,
College Station,Texas
Postcode: 77843-2133
Country: USA
 
Telephone Number: 979-845-5282
Fax Number: 979-845-0627

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: genetic_modification_design
Number of Slides:6
 
Experimental Parameters:
parametergene_knock_out
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: AKSOY: Identification of Genes Differentially Expressed in fry 2-1 Mutants

Slide: Aksoy_1-1_C24 _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 ("Aksoy_1-1_C24 _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: Aksoy_1-1_C24 _Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Genetic Background: Col-0
Growth Conditions:
StratificationKeep petri plates 4 days at 4°C.
Sterilisationseeds were surface sterilized by 70% ethanol and washed with distilled water for several times.
Other Seed PreparationApproximately 200 seeds were sown on each petri dish
ProtocolSeeds were grown on 1/4 strength Murashigee and Skoog basal media containing 0.5 % sucrose, solidified with 0.8 % plant cell tissue grade agar.Approximately 200 seeds were sown on each petri dish and stratified for 4 days at 4°C. Then, they were transferred to a growth chamber providing 16 h of light and 8 h of darkness at 25°C. They were grown for 10 days.
Percentage Agrose0.8
Substrate Sterilising ProcedureSterilized by autoclaving at 121°C under 2kg/cm2 for 25 minutes
Plant Spacing200/plate
Temperature25 °C average, 25 °C day, 25 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: T-DNA knock out mutation in rd29a,LUC
Tissue: whole plant
Additional Organism Information:
Sample DescriptionWhole plantlets were used as sample.
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:1.116968
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-ratio1.149231
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.284739
Spike_AFFX-r2-Bs-dap_5_signal146.929840
NoiseAvg:2.43,Std:0.10,Min:2.2,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_signal71.959801
#P14252
Spike_AFFX-r2-Bs-phe_M_signal137.776489
Corner-Avg:12095,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal166.648849
Spike_AFFX-r2-Ec-bioB_3_signal157.153015
Spike_AFFX-r2-Bs-lys_M_signal59.457142
Spike_AFFX-r2-P1-cre_3_signal7930.947266
Spike_AFFX-r2-Bs-lys_3-5-ratio2.016195
Spike_AFFX-r2-Bs-dap_M_signal708.786255
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.270604
Spike_AFFX-r2-Ec-bioB_avg-signal148.708252
Spike_AFFX-r2-Bs-thr_avg-signal396.793915
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1583.197754
Spike_AFFX-r2-Bs-phe_5_signal128.080109
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2489.723145
RawQ2.519959
Spike_AFFX-r2-Bs-lys_5_signal72.265900
Signal(A)6.847703
%A35.401138
Signal(All)154.524475
Corner+Avg:95,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal516.229675
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal317.317841
Spike_AFFX-r2-Ec-bioD_avg-signal2036.460449
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.481369
Spike_AFFX-r2-Bs-lys_avg-signal92.475060
Spike_AFFX-r2-P1-cre_avg-signal7416.020020
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.117492
Spike_AFFX-r2-Bs-thr_3_signal811.030457
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-signal194.391479
Spike_AFFX-r2-Bs-dap_3_signal1362.782959
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.572591
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal527.944946
#M483
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal145.702118
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.977810
Spike_AFFX-r2-Bs-thr_M_signal307.391418
Signal(P)242.640671
Spike_AFFX-r2-Bs-phe_3-5-ratio2.477495
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9204,Count:9
Spike_AFFX-r2-P1-cre_5_signal6901.092773
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8075
Signal(M)23.381416
BackgroundAvg:61.25,Std:0.93,Min:59.1,Max:64.8
Spike_AFFX-r2-Ec-bioC_avg-signal522.087280
Spike_AFFX-r2-Bs-dap_avg-signal739.499756
Spike_AFFX-r2-Bs-dap_3-5-ratio9.275059
Spike_AFFX-r2-Ec-bioB_5_signal122.322891
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.116968
NF1.000000
HZ4
Tau0.015000

Slide: Aksoy_1-3_C24 _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 ("Aksoy_1-3_C24 _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: Aksoy_1-3_C24 _Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Genetic Background: Col-0
Growth Conditions:
StratificationKeep petri plates 4 days at 4°C.
Sterilisationseeds were surface sterilized by 70% ethanol and washed with distilled water for several times.
Other Seed PreparationApproximately 200 seeds were sown on each petri dish
ProtocolSeeds were grown on 1/4 strength Murashigee and Skoog basal media containing 0.5 % sucrose, solidified with 0.8 % plant cell tissue grade agar.Approximately 200 seeds were sown on each petri dish and stratified for 4 days at 4°C. Then, they were transferred to a growth chamber providing 16 h of light and 8 h of darkness at 25°C. They were grown for 10 days.
Percentage Agrose0.8
Substrate Sterilising ProcedureSterilized by autoclaving at 121°C under 2kg/cm2 for 25 minutes
Plant Spacing200/plate
Temperature25 °C average, 25 °C day, 25 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: T-DNA knock out mutation in rd29a,LUC
Tissue: whole plant
Additional Organism Information:
Sample DescriptionWhole plantlets were used as sample.
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:1.03308
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-ratio1.322754
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.232692
Spike_AFFX-r2-Bs-dap_5_signal150.419983
NoiseAvg:2.44,Std:0.06,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_signal75.894554
#P14394
Spike_AFFX-r2-Bs-phe_M_signal136.094437
Corner-Avg:11567,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal149.200745
Spike_AFFX-r2-Ec-bioB_3_signal98.332863
Spike_AFFX-r2-Bs-lys_M_signal59.828934
Spike_AFFX-r2-P1-cre_3_signal7062.835449
Spike_AFFX-r2-Bs-lys_3-5-ratio2.246200
Spike_AFFX-r2-Bs-dap_M_signal846.620544
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio12.298387
Spike_AFFX-r2-Ec-bioB_avg-signal109.101479
Spike_AFFX-r2-Bs-thr_avg-signal447.074432
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1249.415649
Spike_AFFX-r2-Bs-phe_5_signal125.899246
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1968.481445
RawQ2.370853
Spike_AFFX-r2-Bs-lys_5_signal62.658073
Signal(A)6.170459
%A34.743534
Signal(All)151.848923
Corner+Avg:97,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal411.778381
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal354.674835
Spike_AFFX-r2-Ec-bioD_avg-signal1608.948486
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.103901
Spike_AFFX-r2-Bs-lys_avg-signal87.743187
Spike_AFFX-r2-P1-cre_avg-signal6201.165039
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.152565
Spike_AFFX-r2-Bs-thr_3_signal933.380554
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-signal205.556168
Spike_AFFX-r2-Bs-dap_3_signal1432.373413
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.575522
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal459.606537
#M491
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal140.742554
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.895937
Spike_AFFX-r2-Bs-thr_M_signal331.948151
Signal(P)236.469452
Spike_AFFX-r2-Bs-phe_3-5-ratio2.817132
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8819,Count:9
Spike_AFFX-r2-P1-cre_5_signal5339.494141
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7925
Signal(M)22.468113
BackgroundAvg:60.14,Std:0.39,Min:58.5,Max:61.0
Spike_AFFX-r2-Ec-bioC_avg-signal435.692444
Spike_AFFX-r2-Bs-dap_avg-signal809.804626
Spike_AFFX-r2-Bs-dap_3-5-ratio9.522494
Spike_AFFX-r2-Ec-bioB_5_signal79.770836
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.033080
NF1.000000
HZ4
Tau0.015000

Slide: Aksoy_1-5_C24 _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 ("Aksoy_1-5_C24 _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: Aksoy_1-5_C24 _Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code:
Genetic Background: Col-0
Growth Conditions:
StratificationKeep petri plates 4 days at 4°C.
Sterilisationseeds were surface sterilized by 70% ethanol and washed with distilled water for several times.
Other Seed PreparationApproximately 200 seeds were sown on each petri dish
ProtocolSeeds were grown on 1/4 strength Murashigee and Skoog basal media containing 0.5 % sucrose, solidified with 0.8 % plant cell tissue grade agar.Approximately 200 seeds were sown on each petri dish and stratified for 4 days at 4°C. Then, they were transferred to a growth chamber providing 16 h of light and 8 h of darkness at 25°C. They were grown for 10 days.
Percentage Agrose0.8
Substrate Sterilising ProcedureSterilized by autoclaving at 121°C under 2kg/cm2 for 25 minutes
Plant Spacing200/plate
Temperature25 °C average, 25 °C day, 25 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: T-DNA knock out mutation in rd29a,LUC
Tissue: whole plant
Additional Organism Information:
Sample DescriptionWhole plantlets were used as sample.
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:0.894704
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-ratio1.247901
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.390244
Spike_AFFX-r2-Bs-dap_5_signal154.055344
NoiseAvg:2.51,Std:0.06,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_signal79.880753
#P14714
Spike_AFFX-r2-Bs-phe_M_signal119.147346
Corner-Avg:13032,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal144.985062
Spike_AFFX-r2-Ec-bioB_3_signal121.487457
Spike_AFFX-r2-Bs-lys_M_signal60.545391
Spike_AFFX-r2-P1-cre_3_signal7109.496582
Spike_AFFX-r2-Bs-lys_3-5-ratio2.807206
Spike_AFFX-r2-Bs-dap_M_signal723.916748
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.784861
Spike_AFFX-r2-Ec-bioB_avg-signal117.952736
Spike_AFFX-r2-Bs-thr_avg-signal361.541656
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1288.171021
Spike_AFFX-r2-Bs-phe_5_signal111.635368
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2179.381592
RawQ2.482536
Spike_AFFX-r2-Bs-lys_5_signal52.317348
Signal(A)5.547444
%A33.331871
Signal(All)152.259674
Corner+Avg:112,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal440.609589
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal308.478943
Spike_AFFX-r2-Ec-bioD_avg-signal1733.776367
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.506798
Spike_AFFX-r2-Bs-lys_avg-signal86.576103
Spike_AFFX-r2-P1-cre_avg-signal6403.329590
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.161333
Spike_AFFX-r2-Bs-thr_3_signal701.741272
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-signal179.753891
Spike_AFFX-r2-Bs-dap_3_signal1391.339966
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.691842
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal455.155853
#M493
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal146.865555
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.968041
Spike_AFFX-r2-Bs-thr_M_signal303.003021
Signal(P)232.493256
Spike_AFFX-r2-Bs-phe_3-5-ratio2.763273
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10265,Count:9
Spike_AFFX-r2-P1-cre_5_signal5697.162598
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7603
Signal(M)20.202934
BackgroundAvg:63.57,Std:0.46,Min:62.3,Max:64.6
Spike_AFFX-r2-Ec-bioC_avg-signal447.882721
Spike_AFFX-r2-Bs-dap_avg-signal756.437439
Spike_AFFX-r2-Bs-dap_3-5-ratio9.031429
Spike_AFFX-r2-Ec-bioB_5_signal87.385681
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.894704
NF1.000000
HZ4
Tau0.015000

Slide: Aksoy_1-2_fry2-1 _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 ("Aksoy_1-2_fry2-1 _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: Aksoy_1-2_fry2-1 _Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: fry 2-1
Stock Code:
Growth Conditions:
StratificationKeep petri plates 4 days at 4°C.
Sterilisationseeds were surface sterilized by 70% ethanol and washed with distilled water for several times.
Other Seed PreparationApproximately 200 seeds were sown on each petri dish
ProtocolSeeds were grown on 1/4 strength Murashigee and Skoog basal media containing 0.5 % sucrose, solidified with 0.8 % plant cell tissue grade agar.Approximately 200 seeds were sown on each petri dish and stratified for 4 days at 4°C. Then, they were transferred to a growth chamber providing 16 h of light and 8 h of darkness at 25°C. They were grown for 10 days.
Percentage Agrose0.8
Substrate Sterilising ProcedureSterilized by autoclaving at 121°C under 2kg/cm2 for 25 minutes
Plant Spacing200/plate
Temperature25 °C average, 25 °C day, 25 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: EMS induced mutation mutation in FRY 2
Tissue: whole plant
Additional Organism Information:
Sample DescriptionWhole plantlets were used as sample.
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:1.688068
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-ratio1.125200
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.112819
Spike_AFFX-r2-Bs-dap_5_signal175.303375
NoiseAvg:2.47,Std:0.07,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_signal69.676422
#P12926
Spike_AFFX-r2-Bs-phe_M_signal136.721741
Corner-Avg:11051,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal145.088745
Spike_AFFX-r2-Ec-bioB_3_signal144.750259
Spike_AFFX-r2-Bs-lys_M_signal62.640820
Spike_AFFX-r2-P1-cre_3_signal7891.156250
Spike_AFFX-r2-Bs-lys_3-5-ratio2.410172
Spike_AFFX-r2-Bs-dap_M_signal630.187256
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.291177
Spike_AFFX-r2-Ec-bioB_avg-signal139.971420
Spike_AFFX-r2-Bs-thr_avg-signal353.513458
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1440.632690
Spike_AFFX-r2-Bs-phe_5_signal136.307098
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2490.034424
RawQ2.470732
Spike_AFFX-r2-Bs-lys_5_signal55.714302
Signal(A)9.912435
%A40.775974
Signal(All)159.650253
Corner+Avg:85,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal606.388916
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal219.986526
Spike_AFFX-r2-Ec-bioD_avg-signal1965.333496
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P56.668129
Spike_AFFX-r2-Bs-lys_avg-signal84.212059
Spike_AFFX-r2-P1-cre_avg-signal7452.135742
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.555897
Spike_AFFX-r2-Bs-thr_3_signal647.375977
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-signal164.338455
Spike_AFFX-r2-Bs-dap_3_signal1128.564331
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.728431
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal501.213074
#M583
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal134.281036
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.209843
Spike_AFFX-r2-Bs-thr_M_signal343.488037
Signal(P)273.116852
Spike_AFFX-r2-Bs-phe_3-5-ratio1.613904
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9027,Count:9
Spike_AFFX-r2-P1-cre_5_signal7013.115234
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9301
Signal(M)32.793129
BackgroundAvg:61.07,Std:0.75,Min:59.7,Max:62.7
Spike_AFFX-r2-Ec-bioC_avg-signal553.801025
Spike_AFFX-r2-Bs-dap_avg-signal644.684998
Spike_AFFX-r2-Bs-dap_3-5-ratio6.437778
Spike_AFFX-r2-Ec-bioB_5_signal130.075272
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.688068
NF1.000000
HZ4
Tau0.015000

Slide: Aksoy_1-4_fry2-1 _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 ("Aksoy_1-4_fry2-1 _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: Aksoy_1-4_fry2-1 _Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: fry 2-1
Stock Code:
Growth Conditions:
StratificationKeep petri plates 4 days at 4°C.
Sterilisationseeds were surface sterilized by 70% ethanol and washed with distilled water for several times.
Other Seed PreparationApproximately 200 seeds were sown on each petri dish
ProtocolSeeds were grown on 1/4 strength Murashigee and Skoog basal media containing 0.5 % sucrose, solidified with 0.8 % plant cell tissue grade agar.Approximately 200 seeds were sown on each petri dish and stratified for 4 days at 4°C. Then, they were transferred to a growth chamber providing 16 h of light and 8 h of darkness at 25°C. They were grown for 10 days.
Percentage Agrose0.8
Substrate Sterilising ProcedureSterilized by autoclaving at 121°C under 2kg/cm2 for 25 minutes
Plant Spacing200/plate
Temperature25 °C average, 25 °C day, 25 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: EMS induced mutation mutation in FRY 2
Tissue: whole plant
Additional Organism Information:
Sample DescriptionWhole plantlets were used as sample.
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:1.150751
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-ratio1.269851
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.343191
Spike_AFFX-r2-Bs-dap_5_signal171.883545
NoiseAvg:2.40,Std:0.06,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_signal72.508148
#P13909
Spike_AFFX-r2-Bs-phe_M_signal136.826263
Corner-Avg:12465,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal172.066055
Spike_AFFX-r2-Ec-bioB_3_signal141.258942
Spike_AFFX-r2-Bs-lys_M_signal48.624428
Spike_AFFX-r2-P1-cre_3_signal8972.870117
Spike_AFFX-r2-Bs-lys_3-5-ratio2.047771
Spike_AFFX-r2-Bs-dap_M_signal637.425476
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.159186
Spike_AFFX-r2-Ec-bioB_avg-signal139.497223
Spike_AFFX-r2-Bs-thr_avg-signal316.584839
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1580.595581
Spike_AFFX-r2-Bs-phe_5_signal109.813416
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2458.842773
RawQ2.484921
Spike_AFFX-r2-Bs-lys_5_signal49.982525
Signal(A)7.245931
%A36.953091
Signal(All)158.668060
Corner+Avg:97,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal576.284546
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal258.265717
Spike_AFFX-r2-Ec-bioD_avg-signal2019.719238
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.977642
Spike_AFFX-r2-Bs-lys_avg-signal66.986572
Spike_AFFX-r2-P1-cre_avg-signal8019.476563
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.069268
Spike_AFFX-r2-Bs-thr_3_signal591.607483
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-signal168.301804
Spike_AFFX-r2-Bs-dap_3_signal1186.210449
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.555643
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal550.290344
#M472
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal102.352760
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.047237
Spike_AFFX-r2-Bs-thr_M_signal285.638885
Signal(P)254.962860
Spike_AFFX-r2-Bs-phe_3-5-ratio2.351859
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10069,Count:9
Spike_AFFX-r2-P1-cre_5_signal7066.082520
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8429
Signal(M)25.135891
BackgroundAvg:62.17,Std:0.45,Min:60.2,Max:63.1
Spike_AFFX-r2-Ec-bioC_avg-signal563.287476
Spike_AFFX-r2-Bs-dap_avg-signal665.173157
Spike_AFFX-r2-Bs-dap_3-5-ratio6.901245
Spike_AFFX-r2-Ec-bioB_5_signal105.166656
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.150751
NF1.000000
HZ4
Tau0.015000

Slide: Aksoy_1-6_fry2-1 _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 ("Aksoy_1-6_fry2-1 _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: Aksoy_1-6_fry2-1 _Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: fry 2-1
Stock Code:
Growth Conditions:
StratificationKeep petri plates 4 days at 4°C.
Sterilisationseeds were surface sterilized by 70% ethanol and washed with distilled water for several times.
Other Seed PreparationApproximately 200 seeds were sown on each petri dish
ProtocolSeeds were grown on 1/4 strength Murashigee and Skoog basal media containing 0.5 % sucrose, solidified with 0.8 % plant cell tissue grade agar.Approximately 200 seeds were sown on each petri dish and stratified for 4 days at 4°C. Then, they were transferred to a growth chamber providing 16 h of light and 8 h of darkness at 25°C. They were grown for 10 days.
Percentage Agrose0.8
Substrate Sterilising ProcedureSterilized by autoclaving at 121°C under 2kg/cm2 for 25 minutes
Plant Spacing200/plate
Temperature25 °C average, 25 °C day, 25 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: EMS induced mutation mutation in FRY 2
Tissue: whole plant
Additional Organism Information:
Sample DescriptionWhole plantlets were used as sample.
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:1.025556
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-ratio1.186187
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.425805
Spike_AFFX-r2-Bs-dap_5_signal170.246078
NoiseAvg:2.35,Std:0.08,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_signal82.595306
#P14187
Spike_AFFX-r2-Bs-phe_M_signal126.356773
Corner-Avg:12447,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal149.351929
Spike_AFFX-r2-Ec-bioB_3_signal136.060684
Spike_AFFX-r2-Bs-lys_M_signal46.310555
Spike_AFFX-r2-P1-cre_3_signal8294.163086
Spike_AFFX-r2-Bs-lys_3-5-ratio2.243587
Spike_AFFX-r2-Bs-dap_M_signal687.091553
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.185583
Spike_AFFX-r2-Ec-bioB_avg-signal126.946625
Spike_AFFX-r2-Bs-thr_avg-signal312.613617
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1615.331909
Spike_AFFX-r2-Bs-phe_5_signal117.172653
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2484.218262
RawQ2.346650
Spike_AFFX-r2-Bs-lys_5_signal53.877872
Signal(A)5.954592
%A35.637878
Signal(All)157.462540
Corner+Avg:103,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal516.112427
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal211.214539
Spike_AFFX-r2-Ec-bioD_avg-signal2049.775146
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.196404
Spike_AFFX-r2-Bs-lys_avg-signal73.689362
Spike_AFFX-r2-P1-cre_avg-signal7643.226563
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.165717
Spike_AFFX-r2-Bs-thr_3_signal593.495422
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-signal151.581314
Spike_AFFX-r2-Bs-dap_3_signal1307.806274
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.537900
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal500.357422
#M494
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal120.879669
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.031487
Spike_AFFX-r2-Bs-thr_M_signal261.750061
Signal(P)249.024811
Spike_AFFX-r2-Bs-phe_3-5-ratio1.802592
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9776,Count:9
Spike_AFFX-r2-P1-cre_5_signal6992.290527
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8129
Signal(M)21.053795
BackgroundAvg:59.35,Std:0.50,Min:57.2,Max:60.3
Spike_AFFX-r2-Ec-bioC_avg-signal508.234924
Spike_AFFX-r2-Bs-dap_avg-signal721.714600
Spike_AFFX-r2-Bs-dap_3-5-ratio7.681859
Spike_AFFX-r2-Ec-bioB_5_signal95.427284
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.025556
NF1.000000
HZ4
Tau0.015000


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