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Experiment: Group II-A WRKY transcription factors and early leaf senescence

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-397

In our laboratory we are interested in studying the functions of WRKY zink finger type transcription factors. There are 74 members of this gene family in Arabidopsis. WRKY factors are key regulators of distinct plant defense responses and are involved in certain developmental programs e.g. plant senescence. We would like to determine the functions of a small sub-group (group II-a) of WRKY factors. Our aim to compare and contrast the gene expression profiles of 35 days-old untreated wild type and WRKY T-DNA knockout plants grown in a growth chamber under long day growth conditions. All plants chosen at this stage showed slight yellowing of the first two to four leaves.

About the Experimenter

Name:Dr. Bekir Uelker
Head of Lab Name:Dr. Imre Somssich
Lab: Somsissich Lab
Institute: Max-Planck-Institute for Plant Breeding Research
Address:Department of Plant Microbe Interactions
Carl-von-Linne-Weg 10
Cologne
Postcode: 50829
Country: Germany
 
Telephone Number: 49-221-5062-310
Fax Number: 49-221-5062-353

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:8
 
Experimental Parameters:
parametergene_knock_out
Quality Control Measures Taken:
no-plants-pooled3
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Uelker: Group II-A WRKY transcription factors and early leaf senescence_genome

Slide: Ulker_1-1_WT-Col-0-L_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 ("Ulker_1-1_WT-Col-0-L_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: Ulker_1-1_WT-Col-0-L_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
locationGrowth chamber
AtmosphereNormal
Humidity70%
Temperature22C day 19C night
Lighting(Source: Fluorescent lamps)14 hours light and 8 hour dark
MediumSpecial substrate from Stender Germany containing 70%white turf 20%vermiculite (3-6mm) and 10% sand. The substrate is autoclaved two times with 2 days interval.
TreatmentConfidor WG70 Bayer Germany containing 70% imidacloprid (12g/m3 soil)
NutrientsOsmocote Plus mini containing 16%N 8%P 11%K and 2% micronutrients (100ml/m3 soil)
WaterWhen necesssary. Soil was never let to completely dry.
Developmental Stage:
Growth Stage35 days old. Plants just started bolting.
Tissue: Entire rosette excluding the stem and flowers
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: RNA-wizz
Method:
ProtocolThre plants were harvested in the afternoon by immediately freezing in liquid nitrogen. The samples were stored in -80C for one week. The tissue is ground in liquid nitrogen using mortar and pestle. Two grams of ground tissue was used for RNA isolation using the RNA-Wizz method. 100 microgram RNA was further purified using Qiagen RNeasy Plant Mini Kit by passing the RNA from the columns containing DNAseI.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.501503
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:
RawQ3.19
NoiseAvg:4.66,Stdev:0.36,Max:6.5,Min:3.9
BackgroundAvg:87.43,Stdev:1.00,Max:89.3,Min:83.7
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.501503
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Ulker_1-2_WRKY-KO-02_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 ("Ulker_1-2_WRKY-KO-02_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: Ulker_1-2_WRKY-KO-02_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: WRKY T-DNA knockout
Stock Code:
Growth Conditions:
locationGrowth chamber
AtmosphereNormal
Humidity70%
Temperature22C day 19C night
Lighting(Source: Fluorescent lamps)14 hours light and 8 hour dark
MediumSpecial substrate from Stender Germany containing 70%white turf 20%vermiculite (3-6mm) and 10% sand. The substrate is autoclaved two times with 2 days interval.
TreatmentConfidor WG70 Bayer Germany containing 70% imidacloprid (12g/m3 soil)
NutrientsOsmocote Plus mini containing 16%N 8%P 11%K and 2% micronutrients (100ml/m3 soil)
WaterWhen necesssary. Soil was never let to completely dry.
Developmental Stage:
Growth Stage35 days old. Plants just started bolting.
Tissue: Entire rosette excluding the stem and flowers
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: RNA-wizz
Method:
ProtocolThre plants were harvested in the afternoon by immediately freezing in liquid nitrogen. The samples were stored in -80C for one week. The tissue is ground in liquid nitrogen using mortar and pestle. Two grams of ground tissue was used for RNA isolation using the RNA-Wizz method. 100 microgram RNA was further purified using Qiagen RNeasy Plant Mini Kit by passing the RNA from the columns containing DNAseI.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.464144
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:
RawQ3.21
NoiseAvg:4.67,Stdev:0.26,Max:5.5,Min:4.2
BackgroundAvg:93.59,Stdev:1.01,Max:96.3,Min:90.9
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.464144
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Ulker_1-3_WRKY-KO-07_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 ("Ulker_1-3_WRKY-KO-07_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: Ulker_1-3_WRKY-KO-07_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: WRKY T-DNA knockout
Stock Code:
Growth Conditions:
locationGrowth chamber
AtmosphereNormal
Humidity70%
Temperature22C day 19C night
Lighting(Source: Fluorescent lamps)14 hours light and 8 hour dark
MediumSpecial substrate from Stender Germany containing 70%white turf 20%vermiculite (3-6mm) and 10% sand. The substrate is autoclaved two times with 2 days interval.
TreatmentConfidor WG70 Bayer Germany containing 70% imidacloprid (12g/m3 soil)
NutrientsOsmocote Plus mini containing 16%N 8%P 11%K and 2% micronutrients (100ml/m3 soil)
WaterWhen necesssary. Soil was never let to completely dry.
Developmental Stage:
Growth Stage35 days old. Plants just started bolting.
Tissue: Entire rosette excluding the stem and flowers
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: RNA-wizz
Method:
ProtocolThre plants were harvested in the afternoon by immediately freezing in liquid nitrogen. The samples were stored in -80C for one week. The tissue is ground in liquid nitrogen using mortar and pestle. Two grams of ground tissue was used for RNA isolation using the RNA-Wizz method. 100 microgram RNA was further purified using Qiagen RNeasy Plant Mini Kit by passing the RNA from the columns containing DNAseI.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.372122
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:
RawQ3.44
NoiseAvg:5.06,Stdev:0.15,Max:5.5,Min:4.6
BackgroundAvg:98.31,Stdev:1.32,Max:101.4,Min:95.0
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.372122
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Ulker_1-4_WRKY-KO-54_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 ("Ulker_1-4_WRKY-KO-54_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: Ulker_1-4_WRKY-KO-54_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: WRKY T-DNA knockout
Stock Code:
Growth Conditions:
locationGrowth chamber
AtmosphereNormal
Humidity70%
Temperature22C day 19C night
Lighting(Source: Fluorescent lamps)14 hours light and 8 hour dark
MediumSpecial substrate from Stender Germany containing 70%white turf 20%vermiculite (3-6mm) and 10% sand. The substrate is autoclaved two times with 2 days interval.
TreatmentConfidor WG70 Bayer Germany containing 70% imidacloprid (12g/m3 soil)
NutrientsOsmocote Plus mini containing 16%N 8%P 11%K and 2% micronutrients (100ml/m3 soil)
WaterWhen necesssary. Soil was never let to completely dry.
Developmental Stage:
Growth Stage35 days old. Plants just started bolting.
Tissue: Entire rosette excluding the stem and flowers
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: RNA-wizz
Method:
ProtocolThre plants were harvested in the afternoon by immediately freezing in liquid nitrogen. The samples were stored in -80C for one week. The tissue is ground in liquid nitrogen using mortar and pestle. Two grams of ground tissue was used for RNA isolation using the RNA-Wizz method. 100 microgram RNA was further purified using Qiagen RNeasy Plant Mini Kit by passing the RNA from the columns containing DNAseI.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.380642
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:
RawQ2.87
NoiseAvg:4.04,Stdev:0.09,Max:4.3,Min:3.6
BackgroundAvg:74.67,Stdev:1.10,Max:76.7,Min:72.0
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.380642
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Ulker_1-5_WRKY-KO-40_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 ("Ulker_1-5_WRKY-KO-40_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: Ulker_1-5_WRKY-KO-40_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: WRKY T-DNA knockout
Stock Code:
Growth Conditions:
locationGrowth chamber
AtmosphereNormal
Humidity70%
Temperature22C day 19C night
Lighting(Source: Fluorescent lamps)14 hours light and 8 hour dark
MediumSpecial substrate from Stender Germany containing 70%white turf 20%vermiculite (3-6mm) and 10% sand. The substrate is autoclaved two times with 2 days interval.
TreatmentConfidor WG70 Bayer Germany containing 70% imidacloprid (12g/m3 soil)
NutrientsOsmocote Plus mini containing 16%N 8%P 11%K and 2% micronutrients (100ml/m3 soil)
WaterWhen necesssary. Soil was never let to completely dry.
Developmental Stage:
Growth Stage35 days old. Plants just started bolting.
Tissue: Entire rosette excluding the stem and flowers
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: RNA-wizz
Method:
ProtocolThre plants were harvested in the afternoon by immediately freezing in liquid nitrogen. The samples were stored in -80C for one week. The tissue is ground in liquid nitrogen using mortar and pestle. Two grams of ground tissue was used for RNA isolation using the RNA-Wizz method. 100 microgram RNA was further purified using Qiagen RNeasy Plant Mini Kit by passing the RNA from the columns containing DNAseI.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.362336
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:
RawQ3.23
NoiseAvg:5.33,Stdev:0.12,Max:5.8,Min:5.0
BackgroundAvg:86.15,Stdev:1.64,Max:88.4,Min:82.0
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.362336
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Ulker_1-6_WRKY-KO-30_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 ("Ulker_1-6_WRKY-KO-30_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: Ulker_1-6_WRKY-KO-30_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: WRKY T-DNA knockout
Stock Code:
Growth Conditions:
locationGrowth chamber
AtmosphereNormal
Humidity70%
Temperature22C day 19C night
Lighting(Source: Fluorescent lamps)14 hours light and 8 hour dark
MediumSpecial substrate from Stender Germany containing 70%white turf 20%vermiculite (3-6mm) and 10% sand. The substrate is autoclaved two times with 2 days interval.
TreatmentConfidor WG70 Bayer Germany containing 70% imidacloprid (12g/m3 soil)
NutrientsOsmocote Plus mini containing 16%N 8%P 11%K and 2% micronutrients (100ml/m3 soil)
WaterWhen necesssary. Soil was never let to completely dry.
Developmental Stage:
Growth Stage35 days old. Plants just started bolting.
Tissue: Entire rosette excluding the stem and flowers
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: RNA-wizz
Method:
ProtocolThre plants were harvested in the afternoon by immediately freezing in liquid nitrogen. The samples were stored in -80C for one week. The tissue is ground in liquid nitrogen using mortar and pestle. Two grams of ground tissue was used for RNA isolation using the RNA-Wizz method. 100 microgram RNA was further purified using Qiagen RNeasy Plant Mini Kit by passing the RNA from the columns containing DNAseI.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.522867
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:
RawQ2.14
NoiseAvg:2.93,Stdev:0.07,Max:3.1,Min:2.8
BackgroundAvg:52.94,Stdev:0.67,Max:54.2,Min:51.4
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.522867
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Ulker_1-7_WRKY-KO-56_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 ("Ulker_1-7_WRKY-KO-56_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: Ulker_1-7_WRKY-KO-56_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: WRKY T-DNA knockout
Stock Code:
Growth Conditions:
locationGrowth chamber
AtmosphereNormal
Humidity70%
Temperature22C day 19C night
Lighting(Source: Fluorescent lamps)14 hours light and 8 hour dark
MediumSpecial substrate from Stender Germany containing 70%white turf 20%vermiculite (3-6mm) and 10% sand. The substrate is autoclaved two times with 2 days interval.
TreatmentConfidor WG70 Bayer Germany containing 70% imidacloprid (12g/m3 soil)
NutrientsOsmocote Plus mini containing 16%N 8%P 11%K and 2% micronutrients (100ml/m3 soil)
WaterWhen necesssary. Soil was never let to completely dry.
Developmental Stage:
Growth Stage35 days old. Plants just started bolting.
Tissue: Entire rosette excluding the stem and flowers
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: RNA-wizz
Method:
ProtocolThre plants were harvested in the afternoon by immediately freezing in liquid nitrogen. The samples were stored in -80C for one week. The tissue is ground in liquid nitrogen using mortar and pestle. Two grams of ground tissue was used for RNA isolation using the RNA-Wizz method. 100 microgram RNA was further purified using Qiagen RNeasy Plant Mini Kit by passing the RNA from the columns containing DNAseI.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.414819
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:
RawQ4.41
NoiseAvg:10.07,Stdev:0.35,Max:10.9,Min:9.0
BackgroundAvg:136.06,Stdev:2.80,Max:142.9,Min:129.9
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.414819
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Ulker_1-8_WT_Col-0-S_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 ("Ulker_1-8_WT_Col-0-S_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: Ulker_1-8_WT_Col-0-S_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
locationGrowth chamber
AtmosphereNormal
Humidity70%
Temperature22C day 19C night
Lighting(Source: Fluorescent lamps)14 hours light and 8 hour dark
MediumSpecial substrate from Stender Germany containing 70%white turf 20%vermiculite (3-6mm) and 10% sand. The substrate is autoclaved two times with 2 days interval.
TreatmentConfidor WG70 Bayer Germany containing 70% imidacloprid (12g/m3 soil)
NutrientsOsmocote Plus mini containing 16%N 8%P 11%K and 2% micronutrients (100ml/m3 soil)
WaterWhen necesssary. Soil was never let to completely dry.
Developmental Stage:
Growth Stage35 days old. Plants just started bolting.
Tissue: Entire rosette excluding the stem and flowers
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: RNA-wizz
Method:
ProtocolThre plants were harvested in the afternoon by immediately freezing in liquid nitrogen. The samples were stored in -80C for one week. The tissue is ground in liquid nitrogen using mortar and pestle. Two grams of ground tissue was used for RNA isolation using the RNA-Wizz method. 100 microgram RNA was further purified using Qiagen RNeasy Plant Mini Kit by passing the RNA from the columns containing DNAseI.
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceSubmitter

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:0.411864
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:
RawQ3.34
NoiseAvg:4.77,Stdev:0.15,Max:5.2,Min:4.4
BackgroundAvg:97.01,Stdev:0.85,Max:98.7,Min:94.7
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.411864
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015


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