NASC's International Affymetrix Service

AI logo

NASCArrays

home, selection, spot history, gene swinger, two gene scatterplot, digital northern, bulk gene download, tutorial, help, Affymetrix site, NASC

Experiment: Chemical compound induced somatic embryogenesis in Arabidopsis

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-584

Dry seed of wild-type columbia were germinated in containers with liquid 0.5ms including 1µM 2.4-D.After two days the seedlings were induced with 1µM of 2,4-D incombination with 25µM of the chemical compound. As a control we used seedlings incubated with DMSO.After 0.5hr induction the seedlings were harvested.RNA was extracted using the RNA isolation kit of invitek with an on-column DNAse treatment during the RNA isolation.

About the Experimenter

Name:Mr Tom Stekelenburg
Head of Lab Name: Gerco Angenent
Lab:
Address:Business Unit Bioscience, Plant Research International B.V., Wageningen University
Post box nr 619, Wageningen, , 6700 AP, NETHERLANDS
Postcode:
Country:
 
Telephone Number: 0317-480889

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

About this Experiment

Experiment Type: compound_based_treatment
Number of Slides:6
 
Experimental Parameters:
parametercompound_based_treatment
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Stekelenburg: Chemical compound induced somatic embryogenesis in Arabidopsis

Slide: Stekelenburg_584-6_compound_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 ("Stekelenburg_584-6_compound_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: Stekelenburg_584-6_compound_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia-0
Stock Code:
Growth Conditions:
Protocol
Plant Spacing30/container
Temperature24°C °C average, 24°C °C day, 19°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: After 2 days 25µM Chemical compound was added. 1µM 2.4-D was present from the beginning. seedlings were harvested after 0.5hr of induction.
Additional Organism Information:
Sample DescriptionRNA was isolated from whole 2 day old seedlings.
Other Information:
ecotype_habitat

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:0.311123
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-ratio1.173363
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.696803
Spike_AFFX-r2-Bs-dap_5_signal42.942322
NoiseAvg:3.45,Std:0.12,Min:3.2,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.313906
#P15643
Spike_AFFX-r2-Bs-phe_M_signal11.531484
Corner-Avg:9485,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal70.756836
Spike_AFFX-r2-Ec-bioB_3_signal40.369011
Spike_AFFX-r2-Bs-lys_M_signal7.002290
Spike_AFFX-r2-P1-cre_3_signal2722.374023
Spike_AFFX-r2-Bs-lys_3-5-ratio0.746664
Spike_AFFX-r2-Bs-dap_M_signal91.817665
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.227635
Spike_AFFX-r2-Ec-bioB_avg-signal56.353500
Spike_AFFX-r2-Bs-thr_avg-signal37.328045
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal516.180725
Spike_AFFX-r2-Bs-phe_5_signal19.207106
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal786.633667
RawQ3.077429
Spike_AFFX-r2-Bs-lys_5_signal9.778193
Signal(A)2.311535
%A30.092066
Signal(All)136.652451
Corner+Avg:152,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal204.646454
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal17.624197
Spike_AFFX-r2-Ec-bioD_avg-signal651.407227
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.579567
Spike_AFFX-r2-Bs-lys_avg-signal8.027168
Spike_AFFX-r2-P1-cre_avg-signal2521.260742
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.328365
Spike_AFFX-r2-Bs-thr_3_signal52.655331
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal16.120928
Spike_AFFX-r2-Bs-dap_3_signal132.720322
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.523950
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal209.954422
#M303
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal7.301023
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.974718
Spike_AFFX-r2-Bs-thr_M_signal43.014893
Signal(P)198.057587
Spike_AFFX-r2-Bs-phe_3-5-ratio0.917587
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8363,Count:9
Spike_AFFX-r2-P1-cre_5_signal2320.147217
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6864
Signal(M)9.773197
BackgroundAvg:73.53,Std:0.43,Min:72.6,Max:75.4
Spike_AFFX-r2-Ec-bioC_avg-signal207.300446
Spike_AFFX-r2-Bs-dap_avg-signal89.160103
Spike_AFFX-r2-Bs-dap_3-5-ratio3.090665
Spike_AFFX-r2-Ec-bioB_5_signal57.934650
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.311123
NF1.000000
HZ4
Tau0.015000

Slide: Stekelenburg_584-5_compound_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 ("Stekelenburg_584-5_compound_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: Stekelenburg_584-5_compound_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia-0
Stock Code:
Growth Conditions:
Protocol
Plant Spacing30/container
Temperature24°C °C average, 24°C °C day, 19°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: After 2 days 25µM Chemical compound was added. 1µM 2.4-D was present from the beginning. seedlings were harvested after 0.5hr of induction.
Additional Organism Information:
Sample DescriptionRNA was isolated from whole 2 day old seedlings.
Other Information:
ecotype_habitat

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:0.449655
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-ratio1.069814
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.861564
Spike_AFFX-r2-Bs-dap_5_signal41.018257
NoiseAvg:3.14,Std:0.10,Min:2.9,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal19.133240
#P15244
Spike_AFFX-r2-Bs-phe_M_signal12.271831
Corner-Avg:10003,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal65.411919
Spike_AFFX-r2-Ec-bioB_3_signal57.832226
Spike_AFFX-r2-Bs-lys_M_signal5.596374
Spike_AFFX-r2-P1-cre_3_signal2388.986816
Spike_AFFX-r2-Bs-lys_3-5-ratio0.586317
Spike_AFFX-r2-Bs-dap_M_signal90.647797
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.991062
Spike_AFFX-r2-Ec-bioB_avg-signal63.456287
Spike_AFFX-r2-Bs-thr_avg-signal43.034489
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal537.319153
Spike_AFFX-r2-Bs-phe_5_signal18.791538
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal679.572876
RawQ2.954420
Spike_AFFX-r2-Bs-lys_5_signal9.091329
Signal(A)2.835887
%A31.744848
Signal(All)139.584564
Corner+Avg:160,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal221.111237
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal23.144867
Spike_AFFX-r2-Ec-bioD_avg-signal608.446045
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.830338
Spike_AFFX-r2-Bs-lys_avg-signal6.672700
Spike_AFFX-r2-P1-cre_avg-signal2311.036621
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.424814
Spike_AFFX-r2-Bs-thr_3_signal57.228699
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.069412
Spike_AFFX-r2-Bs-dap_3_signal107.473877
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.264747
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal185.353409
#M325
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal5.330400
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.192917
Spike_AFFX-r2-Bs-thr_M_signal52.741531
Signal(P)207.278091
Spike_AFFX-r2-Bs-phe_3-5-ratio1.231664
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8783,Count:9
Spike_AFFX-r2-P1-cre_5_signal2233.086670
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7241
Signal(M)11.205729
BackgroundAvg:68.97,Std:0.84,Min:67.1,Max:71.3
Spike_AFFX-r2-Ec-bioC_avg-signal203.232330
Spike_AFFX-r2-Bs-dap_avg-signal79.713310
Spike_AFFX-r2-Bs-dap_3-5-ratio2.620147
Spike_AFFX-r2-Ec-bioB_5_signal67.124718
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.449655
NF1.000000
HZ4
Tau0.015000

Slide: Stekelenburg_584-4_compound_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 ("Stekelenburg_584-4_compound_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: Stekelenburg_584-4_compound_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia-0
Stock Code:
Growth Conditions:
Protocol
Plant Spacing30/container
Temperature24°C °C average, 24°C °C day, 19°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: After 2 days 25µM Chemical compound was added. 1µM 2.4-D was present from the beginning. seedlings were harvested after 0.5hr of induction.
Additional Organism Information:
Sample DescriptionRNA was isolated from whole 2 day old seedlings.
Other Information:
ecotype_habitat

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:0.326089
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.869928
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.943611
Spike_AFFX-r2-Bs-dap_5_signal28.491062
NoiseAvg:3.40,Std:0.15,Min:3.1,Max:3.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.822819
#P15406
Spike_AFFX-r2-Bs-phe_M_signal11.036687
Corner-Avg:11024,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal58.944458
Spike_AFFX-r2-Ec-bioB_3_signal48.957973
Spike_AFFX-r2-Bs-lys_M_signal9.011071
Spike_AFFX-r2-P1-cre_3_signal1786.931763
Spike_AFFX-r2-Bs-lys_3-5-ratio0.672259
Spike_AFFX-r2-Bs-dap_M_signal77.873138
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.619398
Spike_AFFX-r2-Ec-bioB_avg-signal53.262024
Spike_AFFX-r2-Bs-thr_avg-signal31.546469
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal462.140472
Spike_AFFX-r2-Bs-phe_5_signal7.015433
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal804.584473
RawQ3.081819
Spike_AFFX-r2-Bs-lys_5_signal8.055251
Signal(A)2.186260
%A31.021482
Signal(All)139.303772
Corner+Avg:184,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal156.527283
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal13.871360
Spike_AFFX-r2-Ec-bioD_avg-signal633.362488
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.540550
Spike_AFFX-r2-Bs-lys_avg-signal7.493845
Spike_AFFX-r2-P1-cre_avg-signal1920.523438
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.437966
Spike_AFFX-r2-Bs-thr_3_signal33.720421
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-signal10.641160
Spike_AFFX-r2-Bs-dap_3_signal107.562294
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.740996
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal177.231049
#M328
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal5.415214
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.883182
Spike_AFFX-r2-Bs-thr_M_signal40.096161
Signal(P)205.037003
Spike_AFFX-r2-Bs-phe_3-5-ratio1.977264
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8442,Count:9
Spike_AFFX-r2-P1-cre_5_signal2054.115234
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7076
Signal(M)9.905143
BackgroundAvg:74.10,Std:1.10,Min:72.1,Max:76.9
Spike_AFFX-r2-Ec-bioC_avg-signal166.879166
Spike_AFFX-r2-Bs-dap_avg-signal71.308830
Spike_AFFX-r2-Bs-dap_3-5-ratio3.775300
Spike_AFFX-r2-Ec-bioB_5_signal51.883644
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.326089
NF1.000000
HZ4
Tau0.015000

Slide: Stekelenburg_584-3_cont_DMSO_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 ("Stekelenburg_584-3_cont_DMSO_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: Stekelenburg_584-3_cont_DMSO_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia-0
Stock Code:
Growth Conditions:
Protocol
Plant Spacing30/container
Temperature24°C °C average, 24°C °C day, 19°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: After 2 days DMSO was added. 1µM 2.4-D was present from the beginning. seedlings were harvested after 0.5hr of induction.
Additional Organism Information:
Sample DescriptionRNA was isolated from whole 2 day old seedlings.
Other Information:
ecotype_habitat

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:0.325783
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-ratio1.016668
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.846542
Spike_AFFX-r2-Bs-dap_5_signal54.255356
NoiseAvg:3.51,Std:0.12,Min:3.3,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal26.460812
#P15403
Spike_AFFX-r2-Bs-phe_M_signal21.785759
Corner-Avg:11099,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal67.213753
Spike_AFFX-r2-Ec-bioB_3_signal48.721348
Spike_AFFX-r2-Bs-lys_M_signal13.259447
Spike_AFFX-r2-P1-cre_3_signal2286.246094
Spike_AFFX-r2-Bs-lys_3-5-ratio0.843169
Spike_AFFX-r2-Bs-dap_M_signal129.903763
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.986282
Spike_AFFX-r2-Ec-bioB_avg-signal57.829494
Spike_AFFX-r2-Bs-thr_avg-signal53.614353
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal458.372589
Spike_AFFX-r2-Bs-phe_5_signal19.113188
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal698.800720
RawQ3.068813
Spike_AFFX-r2-Bs-lys_5_signal14.105370
Signal(A)2.608703
%A31.074091
Signal(All)137.050583
Corner+Avg:175,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal212.812988
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.247433
Spike_AFFX-r2-Ec-bioD_avg-signal578.586670
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.527397
Spike_AFFX-r2-Bs-lys_avg-signal13.086011
Spike_AFFX-r2-P1-cre_avg-signal2267.504883
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.398509
Spike_AFFX-r2-Bs-thr_3_signal79.019447
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal20.715460
Spike_AFFX-r2-Bs-dap_3_signal143.414047
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.524526
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal186.010712
#M319
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal11.893215
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.144090
Spike_AFFX-r2-Bs-thr_M_signal55.362801
Signal(P)201.527817
Spike_AFFX-r2-Bs-phe_3-5-ratio1.111663
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10358,Count:9
Spike_AFFX-r2-P1-cre_5_signal2248.763916
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7088
Signal(M)10.972689
BackgroundAvg:77.12,Std:0.87,Min:74.4,Max:79.3
Spike_AFFX-r2-Ec-bioC_avg-signal199.411850
Spike_AFFX-r2-Bs-dap_avg-signal109.191063
Spike_AFFX-r2-Bs-dap_3-5-ratio2.643316
Spike_AFFX-r2-Ec-bioB_5_signal57.553371
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.325783
NF1.000000
HZ4
Tau0.015000

Slide: Stekelenburg_584-1_cont_DMSO_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 ("Stekelenburg_584-1_cont_DMSO_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: Stekelenburg_584-1_cont_DMSO_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia-0
Stock Code:
Growth Conditions:
Protocol
Temperature24°C °C average, 24°C °C day, 19°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: After 2 days DMSO was added. 1µM 2.4-D was present from the beginning. seedlings were harvested after 0.5hr of induction.
Additional Organism Information:
Sample DescriptionRNA was isolated from whole 2 day old seedlings.
Other Information:
ecotype_habitat

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:0.314925
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-ratio1.134819
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.680252
Spike_AFFX-r2-Bs-dap_5_signal40.797153
NoiseAvg:3.35,Std:0.10,Min:3.1,Max:3.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal17.908064
#P15365
Spike_AFFX-r2-Bs-phe_M_signal8.989465
Corner-Avg:11401,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal68.689507
Spike_AFFX-r2-Ec-bioB_3_signal43.180088
Spike_AFFX-r2-Bs-lys_M_signal9.009969
Spike_AFFX-r2-P1-cre_3_signal2629.512939
Spike_AFFX-r2-Bs-lys_3-5-ratio1.294447
Spike_AFFX-r2-Bs-dap_M_signal89.915154
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.473572
Spike_AFFX-r2-Ec-bioB_avg-signal58.448730
Spike_AFFX-r2-Bs-thr_avg-signal32.602093
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal474.212341
Spike_AFFX-r2-Bs-phe_5_signal17.130760
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal759.799316
RawQ2.932007
Spike_AFFX-r2-Bs-lys_5_signal7.272532
Signal(A)2.466557
%A31.153004
Signal(All)138.939072
Corner+Avg:190,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal238.978531
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal15.409822
Spike_AFFX-r2-Ec-bioD_avg-signal617.005859
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.360809
Spike_AFFX-r2-Bs-lys_avg-signal8.565469
Spike_AFFX-r2-P1-cre_avg-signal2473.317383
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.486190
Spike_AFFX-r2-Bs-thr_3_signal44.296886
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-signal13.843349
Spike_AFFX-r2-Bs-dap_3_signal114.104561
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.602234
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal207.254059
#M339
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal9.413907
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.153070
Spike_AFFX-r2-Bs-thr_M_signal35.601326
Signal(P)204.883926
Spike_AFFX-r2-Bs-phe_3-5-ratio0.899541
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10157,Count:9
Spike_AFFX-r2-P1-cre_5_signal2317.121826
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7106
Signal(M)10.711675
BackgroundAvg:72.59,Std:0.89,Min:70.4,Max:75.0
Spike_AFFX-r2-Ec-bioC_avg-signal223.116302
Spike_AFFX-r2-Bs-dap_avg-signal81.605621
Spike_AFFX-r2-Bs-dap_3-5-ratio2.796875
Spike_AFFX-r2-Ec-bioB_5_signal63.476601
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.314925
NF1.000000
HZ4
Tau0.015000

Slide: Stekelenburg_584-2_cont_DMSO_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 ("Stekelenburg_584-2_cont_DMSO_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: Stekelenburg_584-2_cont_DMSO_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia-0
Stock Code:
Growth Conditions:
Protocol
Plant Spacing30/container
Temperature24°C °C average, 24°C °C day, 19°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: After 2 days DMSO was added. 1µM 2.4-D was present from the beginning. seedlings were harvested after 0.5hr of induction.
Additional Organism Information:
Sample DescriptionRNA was isolated from whole 2 day old seedlings.
Other Information:
ecotype_habitat

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:0.241773
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-ratio1.175840
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.020326
Spike_AFFX-r2-Bs-dap_5_signal37.880486
NoiseAvg:4.18,Std:0.18,Min:3.8,Max:4.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal14.812277
#P15431
Spike_AFFX-r2-Bs-phe_M_signal13.363079
Corner-Avg:12660,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal66.227341
Spike_AFFX-r2-Ec-bioB_3_signal47.233063
Spike_AFFX-r2-Bs-lys_M_signal7.710394
Spike_AFFX-r2-P1-cre_3_signal2381.178711
Spike_AFFX-r2-Bs-lys_3-5-ratio1.076142
Spike_AFFX-r2-Bs-dap_M_signal86.660759
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.903020
Spike_AFFX-r2-Ec-bioB_avg-signal53.250843
Spike_AFFX-r2-Bs-thr_avg-signal35.091362
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal469.305481
Spike_AFFX-r2-Bs-phe_5_signal10.460897
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal817.323425
RawQ3.341556
Spike_AFFX-r2-Bs-lys_5_signal7.498281
Signal(A)2.499770
%A31.144236
Signal(All)136.712357
Corner+Avg:218,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal175.817978
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal11.449903
Spike_AFFX-r2-Ec-bioD_avg-signal643.314453
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.650154
Spike_AFFX-r2-Bs-lys_avg-signal7.759296
Spike_AFFX-r2-P1-cre_avg-signal2203.132813
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.205612
Spike_AFFX-r2-Bs-thr_3_signal57.812618
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-signal11.757960
Spike_AFFX-r2-Bs-dap_3_signal118.331757
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.741560
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal179.050400
#M275
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal8.069215
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.981947
Spike_AFFX-r2-Bs-thr_M_signal32.649185
Signal(P)200.743256
Spike_AFFX-r2-Bs-phe_3-5-ratio1.094543
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10532,Count:9
Spike_AFFX-r2-P1-cre_5_signal2025.086670
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7104
Signal(M)10.840816
BackgroundAvg:89.18,Std:1.05,Min:86.0,Max:92.0
Spike_AFFX-r2-Ec-bioC_avg-signal177.434189
Spike_AFFX-r2-Bs-dap_avg-signal80.957672
Spike_AFFX-r2-Bs-dap_3-5-ratio3.123818
Spike_AFFX-r2-Ec-bioB_5_signal46.292137
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.241773
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team