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: Compound induction

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-603

wildtype Arabidopsis thaliana (ecotype:columbia) seedlings were induced with compound 5 and B at day 2 to form Somatic embryos. 2.4-D was present from the beginning. After 8 hour induction total seedlings were harvest and total RNA was isolated. The aim of this experiment is to see which genes are upregulated compared to a previous experiment were seedlings were induced with DMSO (control) and C3.

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: Compound induction

Slide: Stekelenburg_603-1_compound-5_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_603-1_compound-5_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_603-1_compound-5_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratification2 days 4°C in liquid
Sterilisation15min 2%bleach 1min 70%etoh 5* wash with sterile MQ
Protocolseedlings were grown in containers with 20ml 0.5MS,in a growth chamber at 24°C on a shaker(100RPM) with 16hr/8hr light/dark conditions.
Substrate Sterilising Procedure15minutes 121°C 1bar
Plant Spacing30/20ml
Temperature24°C °C average, 24°C °C day, 24°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture. Modifications: 1µM 2.4-D added at the beginning at day 2 Compound 3 was added
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: at day 2 25µM Compound 3 was added for 8 hours
Additional Organism Information:
Sample Descriptionvery young just germinated seedling
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:0.341312
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-ratio1.277441
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.771033
Spike_AFFX-r2-Bs-dap_5_signal28.333950
NoiseAvg:3.39,Std:0.07,Min:3.2,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal6.300402
#P15243
Spike_AFFX-r2-Bs-phe_M_signal32.622654
Corner-Avg:16469,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal10.449644
Spike_AFFX-r2-Ec-bioB_3_signal10.260693
Spike_AFFX-r2-Bs-lys_M_signal25.009796
Spike_AFFX-r2-P1-cre_3_signal3190.705078
Spike_AFFX-r2-Bs-lys_3-5-ratio1.414691
Spike_AFFX-r2-Bs-dap_M_signal168.402740
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio16.860460
Spike_AFFX-r2-Ec-bioB_avg-signal8.834653
Spike_AFFX-r2-Bs-thr_avg-signal47.008717
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal678.826599
Spike_AFFX-r2-Bs-phe_5_signal26.721674
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal946.720581
RawQ2.903910
Spike_AFFX-r2-Bs-lys_5_signal25.933495
Signal(A)2.902052
%A31.753616
Signal(All)137.069550
Corner+Avg:272,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal185.326187
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal80.263748
Spike_AFFX-r2-Ec-bioD_avg-signal812.773560
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.825951
Spike_AFFX-r2-Bs-lys_avg-signal29.210394
Spike_AFFX-r2-P1-cre_avg-signal2844.218262
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.420430
Spike_AFFX-r2-Bs-thr_3_signal106.227676
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-signal46.536026
Spike_AFFX-r2-Bs-dap_3_signal375.916046
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.394643
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal171.728226
#M324
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal36.687889
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.079183
Spike_AFFX-r2-Bs-thr_M_signal28.498083
Signal(P)203.469971
Spike_AFFX-r2-Bs-phe_3-5-ratio3.003695
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14000,Count:9
Spike_AFFX-r2-P1-cre_5_signal2497.731201
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7243
Signal(M)12.481885
BackgroundAvg:70.91,Std:0.40,Min:69.2,Max:72.3
Spike_AFFX-r2-Ec-bioC_avg-signal178.527206
Spike_AFFX-r2-Bs-dap_avg-signal190.884232
Spike_AFFX-r2-Bs-dap_3-5-ratio13.267337
Spike_AFFX-r2-Ec-bioB_5_signal5.793621
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.341312
NF1.000000
HZ4
Tau0.015000

Slide: Stekelenburg_603-2_compound-5_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_603-2_compound-5_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_603-2_compound-5_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratification2 days 4°C in liquid
Sterilisation15min 2%bleach 1min 70%etoh 5* wash with sterile MQ
Protocolseedlings were grown in containers with 20ml 0.5MS,in a growth chamber at 24°C on a shaker(100RPM) with 16hr/8hr light/dark conditions.
Substrate Sterilising Procedure15minutes 121°C 1bar
Plant Spacing30/20ml
Temperature24°C °C average, 24°C °C day, 24°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture. Modifications: 1µM 2.4-D added at the beginning at day 2 Compound 3 was added
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: at day 2 25µM Compound 3 was added for 8 hours
Additional Organism Information:
Sample Descriptionvery young just germinated seedling
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:0.500574
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-ratio1.066552
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.698023
Spike_AFFX-r2-Bs-dap_5_signal39.259109
NoiseAvg:3.13,Std:0.15,Min:2.8,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionM
Spike_AFFX-r2-Bs-thr_5_signal9.498236
#P14824
Spike_AFFX-r2-Bs-phe_M_signal36.999565
Corner-Avg:15593,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal10.521749
Spike_AFFX-r2-Ec-bioB_3_signal10.886683
Spike_AFFX-r2-Bs-lys_M_signal25.360170
Spike_AFFX-r2-P1-cre_3_signal3148.817383
Spike_AFFX-r2-Bs-lys_3-5-ratio1.544866
Spike_AFFX-r2-Bs-dap_M_signal198.832626
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio16.366093
Spike_AFFX-r2-Ec-bioB_avg-signal12.334962
Spike_AFFX-r2-Bs-thr_avg-signal64.127472
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal607.214172
Spike_AFFX-r2-Bs-phe_5_signal28.140471
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal985.877258
RawQ2.725666
Spike_AFFX-r2-Bs-lys_5_signal33.168293
Signal(A)4.182617
%A33.511620
Signal(All)139.284042
Corner+Avg:266,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal161.870880
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal79.466393
Spike_AFFX-r2-Ec-bioD_avg-signal796.545715
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.989037
Spike_AFFX-r2-Bs-lys_avg-signal36.589680
Spike_AFFX-r2-P1-cre_avg-signal3050.576172
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.499342
Spike_AFFX-r2-Bs-thr_3_signal155.449005
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal48.202145
Spike_AFFX-r2-Bs-dap_3_signal392.005035
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.623607
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal182.092560
#M342
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal51.240578
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.888948
Spike_AFFX-r2-Bs-thr_M_signal27.435186
Signal(P)211.814392
Spike_AFFX-r2-Bs-phe_3-5-ratio2.823918
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11903,Count:9
Spike_AFFX-r2-P1-cre_5_signal2952.334961
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7644
Signal(M)15.089132
BackgroundAvg:65.46,Std:0.69,Min:62.9,Max:66.9
Spike_AFFX-r2-Ec-bioC_avg-signal171.981720
Spike_AFFX-r2-Bs-dap_avg-signal210.032242
Spike_AFFX-r2-Bs-dap_3-5-ratio9.985072
Spike_AFFX-r2-Ec-bioB_5_signal15.596454
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.500574
NF1.000000
HZ4
Tau0.015000

Slide: Stekelenburg_603-3_compound-5_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_603-3_compound-5_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_603-3_compound-5_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratification2 days 4°C in liquid
Sterilisation15min 2%bleach 1min 70%etoh 5* wash with sterile MQ
Protocolseedlings were grown in containers with 20ml 0.5MS,in a growth chamber at 24°C on a shaker(100RPM) with 16hr/8hr light/dark conditions.
Substrate Sterilising Procedure15minutes 121°C 1bar
Plant Spacing30/20ml
Temperature24°C °C average, 24°C °C day, 24°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture. Modifications: 1µM 2.4-D added at the beginning at day 2 Compound 3 was added
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: at day 2 25µM Compound 3 was added for 8 hours
Additional Organism Information:
Sample Descriptionvery young just germinated seedling
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:0.379201
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-ratio1.172607
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.120295
Spike_AFFX-r2-Bs-dap_5_signal32.708866
NoiseAvg:3.21,Std:0.10,Min:2.9,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.167447
#P15029
Spike_AFFX-r2-Bs-phe_M_signal25.982767
Corner-Avg:16143,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal11.917897
Spike_AFFX-r2-Ec-bioB_3_signal10.363376
Spike_AFFX-r2-Bs-lys_M_signal24.894947
Spike_AFFX-r2-P1-cre_3_signal3060.010254
Spike_AFFX-r2-Bs-lys_3-5-ratio1.435280
Spike_AFFX-r2-Bs-dap_M_signal155.668503
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.856003
Spike_AFFX-r2-Ec-bioB_avg-signal10.510617
Spike_AFFX-r2-Bs-thr_avg-signal42.007938
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal656.872803
Spike_AFFX-r2-Bs-phe_5_signal23.278917
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal961.734131
RawQ2.792424
Spike_AFFX-r2-Bs-lys_5_signal21.503437
Signal(A)3.061189
%A32.753178
Signal(All)137.894363
Corner+Avg:266,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal173.344803
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal59.215385
Spike_AFFX-r2-Ec-bioD_avg-signal809.303467
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.887772
Spike_AFFX-r2-Bs-lys_avg-signal25.753942
Spike_AFFX-r2-P1-cre_avg-signal2834.794922
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.359053
Spike_AFFX-r2-Bs-thr_3_signal88.665825
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-signal36.159023
Spike_AFFX-r2-Bs-dap_3_signal334.972809
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.464110
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal195.019455
#M310
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal30.863445
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.888859
Spike_AFFX-r2-Bs-thr_M_signal29.190544
Signal(P)207.497040
Spike_AFFX-r2-Bs-phe_3-5-ratio2.543735
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13638,Count:9
Spike_AFFX-r2-P1-cre_5_signal2609.579590
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7471
Signal(M)12.991019
BackgroundAvg:69.28,Std:0.71,Min:66.4,Max:70.6
Spike_AFFX-r2-Ec-bioC_avg-signal184.182129
Spike_AFFX-r2-Bs-dap_avg-signal174.450058
Spike_AFFX-r2-Bs-dap_3-5-ratio10.241040
Spike_AFFX-r2-Ec-bioB_5_signal9.250578
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.379201
NF1.000000
HZ4
Tau0.015000

Slide: Stekelenburg_603-4_compound-B_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_603-4_compound-B_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_603-4_compound-B_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratification2 days 4°C in liquid
Sterilisation15min 2%bleach 1min 70%etoh 5* wash with sterile MQ
Protocolseedlings were grown in containers with 20ml 0.5MS,in a growth chamber at 24°C on a shaker(100RPM) with 16hr/8hr light/dark conditions.
Substrate Sterilising Procedure15minutes 121°C 1bar
Plant Spacing30/20ml
Temperature24°C °C average, 24°C °C day, 24°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture. Modifications: 1µM 2.4-D added at the beginning at day 2 DMSO was added
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: at day 2 DMSO was added for 8 hours
Additional Organism Information:
Sample Descriptionvery young just germinated seedling
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:0.306097
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-ratio1.265534
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.033993
Spike_AFFX-r2-Bs-dap_5_signal53.377861
NoiseAvg:3.81,Std:0.07,Min:3.6,Max:4.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal9.137325
#P15156
Spike_AFFX-r2-Bs-phe_M_signal41.168690
Corner-Avg:17377,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal9.194388
Spike_AFFX-r2-Ec-bioB_3_signal9.717189
Spike_AFFX-r2-Bs-lys_M_signal28.059355
Spike_AFFX-r2-P1-cre_3_signal2991.124023
Spike_AFFX-r2-Bs-lys_3-5-ratio1.477066
Spike_AFFX-r2-Bs-dap_M_signal225.705200
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio12.278651
Spike_AFFX-r2-Ec-bioB_avg-signal9.436437
Spike_AFFX-r2-Bs-thr_avg-signal51.245396
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal571.780029
Spike_AFFX-r2-Bs-phe_5_signal37.612179
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal848.473511
RawQ2.925234
Spike_AFFX-r2-Bs-lys_5_signal35.100204
Signal(A)3.502840
%A31.937746
Signal(All)136.405441
Corner+Avg:290,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal156.650040
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal93.509087
Spike_AFFX-r2-Ec-bioD_avg-signal710.126770
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.444542
Spike_AFFX-r2-Bs-lys_avg-signal38.334957
Spike_AFFX-r2-P1-cre_avg-signal2677.325439
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.617712
Spike_AFFX-r2-Bs-thr_3_signal112.194031
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal57.429989
Spike_AFFX-r2-Bs-dap_3_signal437.152283
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.483916
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal164.761276
#M369
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal51.845310
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.950770
Spike_AFFX-r2-Bs-thr_M_signal32.404827
Signal(P)203.280243
Spike_AFFX-r2-Bs-phe_3-5-ratio2.486139
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15621,Count:9
Spike_AFFX-r2-P1-cre_5_signal2363.526855
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7285
Signal(M)13.481811
BackgroundAvg:73.06,Std:1.11,Min:69.7,Max:75.5
Spike_AFFX-r2-Ec-bioC_avg-signal160.705658
Spike_AFFX-r2-Bs-dap_avg-signal238.745117
Spike_AFFX-r2-Bs-dap_3-5-ratio8.189768
Spike_AFFX-r2-Ec-bioB_5_signal9.397735
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.306097
NF1.000000
HZ4
Tau0.015000

Slide: Stekelenburg_603-5_compound-B_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_603-5_compound-B_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_603-5_compound-B_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratification2 days 4°C in liquid
Sterilisation15min 2%bleach 1min 70%etoh 5* wash with sterile MQ
Protocolseedlings were grown in containers with 20ml 0.5MS,in a growth chamber at 24°C on a shaker(100RPM) with 16hr/8hr light/dark conditions.
Substrate Sterilising Procedure15minutes 121°C 1bar
Plant Spacing30/20ml
Temperature24°C °C average, 24°C °C day, 24°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture. Modifications: 1µM 2.4-D added at the beginning at day 2 DMSO was added
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: at day 2 DMSO was added for 8 hours
Additional Organism Information:
Sample Descriptionvery young just germinated seedling
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:0.378385
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-ratio1.214366
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.397615
Spike_AFFX-r2-Bs-dap_5_signal85.382698
NoiseAvg:3.19,Std:0.11,Min:2.9,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_signal10.482992
#P15140
Spike_AFFX-r2-Bs-phe_M_signal62.341534
Corner-Avg:17014,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal14.154175
Spike_AFFX-r2-Ec-bioB_3_signal14.549452
Spike_AFFX-r2-Bs-lys_M_signal39.297810
Spike_AFFX-r2-P1-cre_3_signal3854.005859
Spike_AFFX-r2-Bs-lys_3-5-ratio1.390612
Spike_AFFX-r2-Bs-dap_M_signal311.217529
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio20.408566
Spike_AFFX-r2-Ec-bioB_avg-signal13.037941
Spike_AFFX-r2-Bs-thr_avg-signal95.398827
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal827.934631
Spike_AFFX-r2-Bs-phe_5_signal50.467785
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1180.955078
RawQ2.653612
Spike_AFFX-r2-Bs-lys_5_signal51.106567
Signal(A)3.412886
%A32.117493
Signal(All)139.525726
Corner+Avg:284,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal222.913910
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal125.658478
Spike_AFFX-r2-Ec-bioD_avg-signal1004.444824
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.374397
Spike_AFFX-r2-Bs-lys_avg-signal53.824596
Spike_AFFX-r2-P1-cre_avg-signal3513.841064
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.508111
Spike_AFFX-r2-Bs-thr_3_signal213.942841
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-signal79.489265
Spike_AFFX-r2-Bs-dap_3_signal707.739563
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.426387
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal217.780151
#M344
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal71.069405
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.023573
Spike_AFFX-r2-Bs-thr_M_signal61.770626
Signal(P)208.224411
Spike_AFFX-r2-Bs-phe_3-5-ratio2.489875
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14987,Count:9
Spike_AFFX-r2-P1-cre_5_signal3173.676270
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7326
Signal(M)14.713239
BackgroundAvg:66.66,Std:0.48,Min:65.6,Max:68.2
Spike_AFFX-r2-Ec-bioC_avg-signal220.347031
Spike_AFFX-r2-Bs-dap_avg-signal368.113281
Spike_AFFX-r2-Bs-dap_3-5-ratio8.289028
Spike_AFFX-r2-Ec-bioB_5_signal10.410198
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.378385
NF1.000000
HZ4
Tau0.015000

Slide: Stekelenburg_603-6_compound-B_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_603-6_compound-B_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_603-6_compound-B_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratification2 days 4°C in liquid
Sterilisation15min 2%bleach 1min 70%etoh 5* wash with sterile MQ
Protocolseedlings were grown in containers with 20ml 0.5MS,in a growth chamber at 24°C on a shaker(100RPM) with 16hr/8hr light/dark conditions.
Substrate Sterilising Procedure15minutes 121°C 1bar
Plant Spacing30/20ml
Temperature24°C °C average, 24°C °C day, 24°C °C night
Humidity100% % average, 100% % day, 100% % night
MediumMurashige & Skoog basal salt mixture. Modifications: 1µM 2.4-D added at the beginning at day 2 DMSO was added
Lighting(Source: Unknown. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
in vivo Treatment: at day 2 DMSO was added for 8 hours
Additional Organism Information:
Sample Descriptionvery young just germinated seedling
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:0.303661
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-ratio1.226211
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.185950
Spike_AFFX-r2-Bs-dap_5_signal22.197245
NoiseAvg:3.38,Std:0.11,Min:3.2,Max:3.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.606414
#P15302
Spike_AFFX-r2-Bs-phe_M_signal20.755243
Corner-Avg:16249,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal8.807159
Spike_AFFX-r2-Ec-bioB_3_signal8.167985
Spike_AFFX-r2-Bs-lys_M_signal15.794382
Spike_AFFX-r2-P1-cre_3_signal2842.306885
Spike_AFFX-r2-Bs-lys_3-5-ratio1.508197
Spike_AFFX-r2-Bs-dap_M_signal122.812447
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.685352
Spike_AFFX-r2-Ec-bioB_avg-signal7.954146
Spike_AFFX-r2-Bs-thr_avg-signal29.755257
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal593.541443
Spike_AFFX-r2-Bs-phe_5_signal13.037339
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal827.784241
RawQ2.695327
Spike_AFFX-r2-Bs-lys_5_signal17.327312
Signal(A)2.845233
%A31.446733
Signal(All)136.125626
Corner+Avg:279,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal146.169968
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal45.739937
Spike_AFFX-r2-Ec-bioD_avg-signal710.662842
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.084610
Spike_AFFX-r2-Bs-lys_avg-signal19.751566
Spike_AFFX-r2-P1-cre_avg-signal2580.132813
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.468654
Spike_AFFX-r2-Bs-thr_3_signal59.906506
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal26.510839
Spike_AFFX-r2-Bs-dap_3_signal260.040771
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.394653
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal159.440689
#M335
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.133003
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.916767
Spike_AFFX-r2-Bs-thr_M_signal23.752851
Signal(P)201.313568
Spike_AFFX-r2-Bs-phe_3-5-ratio3.508380
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14091,Count:9
Spike_AFFX-r2-P1-cre_5_signal2317.958496
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7173
Signal(M)12.288299
BackgroundAvg:65.95,Std:0.92,Min:64.1,Max:68.3
Spike_AFFX-r2-Ec-bioC_avg-signal152.805328
Spike_AFFX-r2-Bs-dap_avg-signal135.016815
Spike_AFFX-r2-Bs-dap_3-5-ratio11.715002
Spike_AFFX-r2-Ec-bioB_5_signal6.887296
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.303661
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team