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Experiment: Identification of putative directly-regulated STM target genes

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-592

The KNOX gene SHOOT MERISTEMLESS (STM) encodes a homeodomain trascriptional regulator that is critical for shoot apical meristem (SAM)function in Arabidopsis. To identify target genes, STM function was induced using an STM-GR fusion protein activated by dexamethasone for 3 hours, after which total RNA was isolated and analysed using Affymetrix ATH1 arrays. This was compared to a mock-induced sample. Additionally, STM function was induced with dex in the presence of cycloheximide to identify genes that show differetial regulation in the absence of protein synthesis, which may therefore be directly-regulated STM target genes.

About the Experimenter

Name:Dr Simon Scofield
Head of Lab Name:Prof Jim Murray
Lab:
Address:Molecular Cell Biology Research Group , School of Biosciences, Cardiff University
Cardiff, South Glamorgan, CF10 3US, UNITED KINGDOM
Postcode:
Country:
 
Telephone Number: 02920 879396
Fax Number: 01223 334162

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: gene_knock_in
Number of Slides:12
 
Experimental Parameters:
parametergene_knock_in
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Scofield: Identification of putative directly-regulated STM target genes

Slide: Scofield_592-1_Mock-induced_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 ("Scofield_592-1_Mock-induced_Rep1_ATH1") was made from "" 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: Scofield_592-1_Mock-induced_Rep1_ATH1
Organism:
Stock Code:
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:0.581955
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-ratio1.211430
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.814590
Spike_AFFX-r2-Bs-dap_5_signal33.705494
NoiseAvg:2.88,Std:0.05,Min:2.8,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.307873
#P14097
Spike_AFFX-r2-Bs-phe_M_signal23.913473
Corner-Avg:7220,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal81.539780
Spike_AFFX-r2-Ec-bioB_3_signal57.451981
Spike_AFFX-r2-Bs-lys_M_signal12.255323
Spike_AFFX-r2-P1-cre_3_signal4310.490234
Spike_AFFX-r2-Bs-lys_3-5-ratio2.094451
Spike_AFFX-r2-Bs-dap_M_signal114.373993
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.643888
Spike_AFFX-r2-Ec-bioB_avg-signal69.840149
Spike_AFFX-r2-Bs-thr_avg-signal36.257751
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal763.242432
Spike_AFFX-r2-Bs-phe_5_signal19.588154
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1171.379517
RawQ2.615339
Spike_AFFX-r2-Bs-lys_5_signal10.043041
Signal(A)4.691024
%A36.321789
Signal(All)148.077347
Corner+Avg:128,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal302.665863
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal25.849962
Spike_AFFX-r2-Ec-bioD_avg-signal967.310974
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.801842
Spike_AFFX-r2-Bs-lys_avg-signal14.444341
Spike_AFFX-r2-P1-cre_avg-signal3934.336426
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.876370
Spike_AFFX-r2-Bs-thr_3_signal58.176476
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-signal23.117197
Spike_AFFX-r2-Bs-dap_3_signal137.839325
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.534741
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal326.882874
#M428
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.034658
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.925915
Spike_AFFX-r2-Bs-thr_M_signal40.288898
Signal(P)236.308258
Spike_AFFX-r2-Bs-phe_3-5-ratio1.319673
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4467,Count:9
Spike_AFFX-r2-P1-cre_5_signal3558.182373
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8285
Signal(M)17.620399
BackgroundAvg:61.19,Std:0.25,Min:60.4,Max:62.0
Spike_AFFX-r2-Ec-bioC_avg-signal314.774353
Spike_AFFX-r2-Bs-dap_avg-signal95.306274
Spike_AFFX-r2-Bs-dap_3-5-ratio4.089521
Spike_AFFX-r2-Ec-bioB_5_signal70.528694
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.581955
NF1.000000
HZ4
Tau0.015000

Slide: Scofield_592-2_DEX-induced_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 ("Scofield_592-2_DEX-induced_Rep1_ATH1") was made from "" 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: Scofield_592-2_DEX-induced_Rep1_ATH1
Organism:
Stock Code:
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:0.461943
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-ratio1.427720
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.760132
Spike_AFFX-r2-Bs-dap_5_signal38.537380
NoiseAvg:2.91,Std:0.07,Min:2.7,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal17.613903
#P15032
Spike_AFFX-r2-Bs-phe_M_signal17.826853
Corner-Avg:8482,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal82.671906
Spike_AFFX-r2-Ec-bioB_3_signal56.974350
Spike_AFFX-r2-Bs-lys_M_signal14.806110
Spike_AFFX-r2-P1-cre_3_signal3633.489258
Spike_AFFX-r2-Bs-lys_3-5-ratio1.684478
Spike_AFFX-r2-Bs-dap_M_signal129.049927
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.966844
Spike_AFFX-r2-Ec-bioB_avg-signal71.533180
Spike_AFFX-r2-Bs-thr_avg-signal50.560024
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal586.516846
Spike_AFFX-r2-Bs-phe_5_signal27.066460
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1135.337769
RawQ2.734609
Spike_AFFX-r2-Bs-lys_5_signal13.600662
Signal(A)3.163716
%A32.599735
Signal(All)142.065506
Corner+Avg:142,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal267.849731
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal23.459871
Spike_AFFX-r2-Ec-bioD_avg-signal860.927307
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.900917
Spike_AFFX-r2-Bs-lys_avg-signal17.105597
Spike_AFFX-r2-P1-cre_avg-signal3089.224365
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_signal87.485504
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-signal22.784393
Spike_AFFX-r2-Bs-dap_3_signal192.230804
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.935729
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal237.511169
#M342
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal22.910019
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.127735
Spike_AFFX-r2-Bs-thr_M_signal46.580654
Signal(P)213.728333
Spike_AFFX-r2-Bs-phe_3-5-ratio0.866751
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5797,Count:9
Spike_AFFX-r2-P1-cre_5_signal2544.959473
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7436
Signal(M)12.352069
BackgroundAvg:63.79,Std:0.71,Min:61.6,Max:65.6
Spike_AFFX-r2-Ec-bioC_avg-signal252.680450
Spike_AFFX-r2-Bs-dap_avg-signal119.939369
Spike_AFFX-r2-Bs-dap_3-5-ratio4.988165
Spike_AFFX-r2-Ec-bioB_5_signal74.953278
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.461943
NF1.000000
HZ4
Tau0.015000

Slide: Scofield_592-3_CHX-treated_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 ("Scofield_592-3_CHX-treated_Rep1_ATH1") was made from "" 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: Scofield_592-3_CHX-treated_Rep1_ATH1
Organism:
Stock Code:
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:0.36162
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-ratio1.276785
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.102356
Spike_AFFX-r2-Bs-dap_5_signal12.534479
NoiseAvg:3.25,Std:0.14,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_signal7.228346
#P15455
Spike_AFFX-r2-Bs-phe_M_signal15.357485
Corner-Avg:9196,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal76.818848
Spike_AFFX-r2-Ec-bioB_3_signal61.528675
Spike_AFFX-r2-Bs-lys_M_signal12.796818
Spike_AFFX-r2-P1-cre_3_signal3592.922119
Spike_AFFX-r2-Bs-lys_3-5-ratio2.552262
Spike_AFFX-r2-Bs-dap_M_signal74.886894
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.832180
Spike_AFFX-r2-Ec-bioB_avg-signal64.721046
Spike_AFFX-r2-Bs-thr_avg-signal29.197531
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal656.374207
Spike_AFFX-r2-Bs-phe_5_signal15.060140
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1037.549927
RawQ2.942712
Spike_AFFX-r2-Bs-lys_5_signal9.082130
Signal(A)2.910947
%A30.767208
Signal(All)141.462189
Corner+Avg:147,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal269.361145
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.929758
Spike_AFFX-r2-Ec-bioD_avg-signal846.962036
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.755371
Spike_AFFX-r2-Bs-lys_avg-signal15.019641
Spike_AFFX-r2-P1-cre_avg-signal3203.480713
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.477422
Spike_AFFX-r2-Bs-thr_3_signal49.385361
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-signal17.449127
Spike_AFFX-r2-Bs-dap_3_signal132.289536
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.580729
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal236.548050
#M337
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.179974
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.138716
Spike_AFFX-r2-Bs-thr_M_signal30.978878
Signal(P)207.217392
Spike_AFFX-r2-Bs-phe_3-5-ratio1.456146
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7339,Count:9
Spike_AFFX-r2-P1-cre_5_signal2814.039307
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7018
Signal(M)11.212406
BackgroundAvg:69.93,Std:0.61,Min:68.3,Max:71.4
Spike_AFFX-r2-Ec-bioC_avg-signal252.954590
Spike_AFFX-r2-Bs-dap_avg-signal73.236969
Spike_AFFX-r2-Bs-dap_3-5-ratio10.554051
Spike_AFFX-r2-Ec-bioB_5_signal55.815613
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.361620
NF1.000000
HZ4
Tau0.015000

Slide: Scofield_592-4_CHX+DEX-induced_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 ("Scofield_592-4_CHX+DEX-induced_Rep1_ATH1") was made from "" 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: Scofield_592-4_CHX+DEX-induced_Rep1_ATH1
Organism:
Stock Code:
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:0.408417
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-ratio1.132630
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.908518
Spike_AFFX-r2-Bs-dap_5_signal26.638334
NoiseAvg:2.97,Std:0.08,Min:2.8,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal17.045855
#P15257
Spike_AFFX-r2-Bs-phe_M_signal11.159424
Corner-Avg:7201,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal55.315289
Spike_AFFX-r2-Ec-bioB_3_signal37.688732
Spike_AFFX-r2-Bs-lys_M_signal7.159881
Spike_AFFX-r2-P1-cre_3_signal2437.692871
Spike_AFFX-r2-Bs-lys_3-5-ratio2.547660
Spike_AFFX-r2-Bs-dap_M_signal91.152473
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.599359
Spike_AFFX-r2-Ec-bioB_avg-signal44.829258
Spike_AFFX-r2-Bs-thr_avg-signal47.552032
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal346.751038
Spike_AFFX-r2-Bs-phe_5_signal24.160503
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal740.158020
RawQ2.671628
Spike_AFFX-r2-Bs-lys_5_signal9.504127
Signal(A)3.259957
%A31.626480
Signal(All)140.251678
Corner+Avg:121,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal165.863373
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal19.031319
Spike_AFFX-r2-Ec-bioD_avg-signal543.454529
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.887329
Spike_AFFX-r2-Bs-lys_avg-signal13.625766
Spike_AFFX-r2-P1-cre_avg-signal2294.967285
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.486190
Spike_AFFX-r2-Bs-thr_3_signal78.399994
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-signal18.117083
Spike_AFFX-r2-Bs-dap_3_signal127.973343
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.134552
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal174.792435
#M339
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.213287
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.948916
Spike_AFFX-r2-Bs-thr_M_signal47.210255
Signal(P)207.879135
Spike_AFFX-r2-Bs-phe_3-5-ratio0.787704
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4485,Count:9
Spike_AFFX-r2-P1-cre_5_signal2152.241943
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7214
Signal(M)11.833618
BackgroundAvg:62.35,Std:0.53,Min:61.0,Max:63.8
Spike_AFFX-r2-Ec-bioC_avg-signal170.327911
Spike_AFFX-r2-Bs-dap_avg-signal81.921387
Spike_AFFX-r2-Bs-dap_3-5-ratio4.804104
Spike_AFFX-r2-Ec-bioB_5_signal41.483761
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.408417
NF1.000000
HZ4
Tau0.015000

Slide: Scofield_592-5_Mock-induced_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 ("Scofield_592-5_Mock-induced_Rep2_ATH1") was made from "" 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: Scofield_592-5_Mock-induced_Rep2_ATH1
Organism:
Stock Code:
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:0.562297
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-ratio1.002206
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.712768
Spike_AFFX-r2-Bs-dap_5_signal33.836491
NoiseAvg:2.87,Std:0.10,Min:2.6,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.098880
#P14699
Spike_AFFX-r2-Bs-phe_M_signal24.309460
Corner-Avg:7639,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal65.952316
Spike_AFFX-r2-Ec-bioB_3_signal50.543400
Spike_AFFX-r2-Bs-lys_M_signal12.050937
Spike_AFFX-r2-P1-cre_3_signal2555.158447
Spike_AFFX-r2-Bs-lys_3-5-ratio1.972499
Spike_AFFX-r2-Bs-dap_M_signal101.745605
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.256968
Spike_AFFX-r2-Ec-bioB_avg-signal62.469055
Spike_AFFX-r2-Bs-thr_avg-signal54.329681
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal455.310486
Spike_AFFX-r2-Bs-phe_5_signal19.826681
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal810.233887
RawQ2.758045
Spike_AFFX-r2-Bs-lys_5_signal14.611986
Signal(A)3.631287
%A33.954407
Signal(All)144.301865
Corner+Avg:130,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal263.260529
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal33.629063
Spike_AFFX-r2-Ec-bioD_avg-signal632.772217
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.441032
Spike_AFFX-r2-Bs-lys_avg-signal18.495016
Spike_AFFX-r2-P1-cre_avg-signal2552.345947
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.604559
Spike_AFFX-r2-Bs-thr_3_signal87.801186
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-signal25.921736
Spike_AFFX-r2-Bs-dap_3_signal139.468674
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.779519
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal268.333588
#M366
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.822123
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.981094
Spike_AFFX-r2-Bs-thr_M_signal63.088982
Signal(P)221.628281
Spike_AFFX-r2-Bs-phe_3-5-ratio1.696152
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5573,Count:9
Spike_AFFX-r2-P1-cre_5_signal2549.533447
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7745
Signal(M)15.538960
BackgroundAvg:65.33,Std:0.45,Min:64.2,Max:66.8
Spike_AFFX-r2-Ec-bioC_avg-signal265.797058
Spike_AFFX-r2-Bs-dap_avg-signal91.683594
Spike_AFFX-r2-Bs-dap_3-5-ratio4.121842
Spike_AFFX-r2-Ec-bioB_5_signal70.911453
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.562297
NF1.000000
HZ4
Tau0.015000

Slide: Scofield_592-6_DEX-induced_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 ("Scofield_592-6_DEX-induced_Rep2_ATH1") was made from "" 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: Scofield_592-6_DEX-induced_Rep2_ATH1
Organism:
Stock Code:
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:0.487437
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-ratio0.969902
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.092279
Spike_AFFX-r2-Bs-dap_5_signal51.561657
NoiseAvg:2.92,Std:0.09,Min:2.5,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.405624
#P15051
Spike_AFFX-r2-Bs-phe_M_signal29.536757
Corner-Avg:9721,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal76.825317
Spike_AFFX-r2-Ec-bioB_3_signal64.794434
Spike_AFFX-r2-Bs-lys_M_signal14.316016
Spike_AFFX-r2-P1-cre_3_signal2824.756104
Spike_AFFX-r2-Bs-lys_3-5-ratio1.955420
Spike_AFFX-r2-Bs-dap_M_signal159.494751
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.563284
Spike_AFFX-r2-Ec-bioB_avg-signal66.980049
Spike_AFFX-r2-Bs-thr_avg-signal57.704388
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal529.936096
Spike_AFFX-r2-Bs-phe_5_signal23.651480
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1040.603882
RawQ2.678083
Spike_AFFX-r2-Bs-lys_5_signal17.748684
Signal(A)3.748448
%A32.301620
Signal(All)141.472580
Corner+Avg:149,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal249.040421
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal31.508743
Spike_AFFX-r2-Ec-bioD_avg-signal785.270020
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.984215
Spike_AFFX-r2-Bs-lys_avg-signal22.256945
Spike_AFFX-r2-P1-cre_avg-signal2868.585205
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.714160
Spike_AFFX-r2-Bs-thr_3_signal93.116661
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-signal28.232328
Spike_AFFX-r2-Bs-dap_3_signal230.338379
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.963640
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal208.219727
#M391
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal34.706135
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.196046
Spike_AFFX-r2-Bs-thr_M_signal59.590870
Signal(P)212.194809
Spike_AFFX-r2-Bs-phe_3-5-ratio1.332210
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8083,Count:9
Spike_AFFX-r2-P1-cre_5_signal2912.414307
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7368
Signal(M)14.391088
BackgroundAvg:64.16,Std:0.64,Min:62.8,Max:65.7
Spike_AFFX-r2-Ec-bioC_avg-signal228.630066
Spike_AFFX-r2-Bs-dap_avg-signal147.131592
Spike_AFFX-r2-Bs-dap_3-5-ratio4.467242
Spike_AFFX-r2-Ec-bioB_5_signal59.320412
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.487437
NF1.000000
HZ4
Tau0.015000

Slide: Scofield_592-7_CHX-treated_Rep2_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 ("Scofield_592-7_CHX-treated_Rep2_ATH1") was made from "" 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: Scofield_592-7_CHX-treated_Rep2_ATH1
Organism:
Stock Code:
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:0.448094
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-ratio1.062901
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.926596
Spike_AFFX-r2-Bs-dap_5_signal27.502069
NoiseAvg:3.21,Std:0.09,Min:3.0,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_signal15.660232
#P15074
Spike_AFFX-r2-Bs-phe_M_signal12.457820
Corner-Avg:8810,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal77.314224
Spike_AFFX-r2-Ec-bioB_3_signal54.989067
Spike_AFFX-r2-Bs-lys_M_signal6.933132
Spike_AFFX-r2-P1-cre_3_signal2915.662598
Spike_AFFX-r2-Bs-lys_3-5-ratio1.741482
Spike_AFFX-r2-Bs-dap_M_signal108.076767
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.011080
Spike_AFFX-r2-Ec-bioB_avg-signal63.882854
Spike_AFFX-r2-Bs-thr_avg-signal39.574940
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal589.967407
Spike_AFFX-r2-Bs-phe_5_signal18.039911
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1045.181030
RawQ2.881945
Spike_AFFX-r2-Bs-lys_5_signal15.408059
Signal(A)3.817504
%A32.143795
Signal(All)144.344803
Corner+Avg:145,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal226.102036
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal15.364207
Spike_AFFX-r2-Ec-bioD_avg-signal817.574219
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.085052
Spike_AFFX-r2-Bs-lys_avg-signal16.391352
Spike_AFFX-r2-P1-cre_avg-signal2829.389648
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.771153
Spike_AFFX-r2-Bs-thr_3_signal62.814438
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-signal15.287313
Spike_AFFX-r2-Bs-dap_3_signal133.001938
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.771591
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal222.552689
#M404
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.832863
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.015948
Spike_AFFX-r2-Bs-thr_M_signal40.250156
Signal(P)215.988037
Spike_AFFX-r2-Bs-phe_3-5-ratio0.851679
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6193,Count:9
Spike_AFFX-r2-P1-cre_5_signal2743.116699
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7332
Signal(M)21.562452
BackgroundAvg:69.52,Std:0.67,Min:67.9,Max:71.5
Spike_AFFX-r2-Ec-bioC_avg-signal224.327362
Spike_AFFX-r2-Bs-dap_avg-signal89.526924
Spike_AFFX-r2-Bs-dap_3-5-ratio4.836070
Spike_AFFX-r2-Ec-bioB_5_signal59.345276
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.448094
NF1.000000
HZ4
Tau0.015000

Slide: Scofield_592-8_CHX+DEX-induced_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 ("Scofield_592-8_CHX+DEX-induced_Rep2_ATH1") was made from "" 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: Scofield_592-8_CHX+DEX-induced_Rep2_ATH1
Organism:
Stock Code:
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:0.346111
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-ratio1.229808
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.033260
Spike_AFFX-r2-Bs-dap_5_signal24.073204
NoiseAvg:3.72,Std:0.09,Min:3.3,Max:4.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.819588
#P15306
Spike_AFFX-r2-Bs-phe_M_signal7.138725
Corner-Avg:8827,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal41.832344
Spike_AFFX-r2-Ec-bioB_3_signal34.589211
Spike_AFFX-r2-Bs-lys_M_signal4.716628
Spike_AFFX-r2-P1-cre_3_signal2300.445801
Spike_AFFX-r2-Bs-lys_3-5-ratio1.922458
Spike_AFFX-r2-Bs-dap_M_signal85.090530
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.651106
Spike_AFFX-r2-Ec-bioB_avg-signal36.632450
Spike_AFFX-r2-Bs-thr_avg-signal35.895657
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal303.294647
Spike_AFFX-r2-Bs-phe_5_signal12.231627
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal512.816284
RawQ3.109553
Spike_AFFX-r2-Bs-lys_5_signal7.449429
Signal(A)3.649895
%A31.258221
Signal(All)137.774460
Corner+Avg:141,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal160.708160
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal24.529531
Spike_AFFX-r2-Ec-bioD_avg-signal408.055481
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.102150
Spike_AFFX-r2-Bs-lys_avg-signal8.829091
Spike_AFFX-r2-P1-cre_avg-signal2085.509277
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.639632
Spike_AFFX-r2-Bs-thr_3_signal58.660015
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-signal14.633294
Spike_AFFX-r2-Bs-dap_3_signal124.737244
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.690819
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal136.210297
#M374
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal14.321216
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.179853
Spike_AFFX-r2-Bs-thr_M_signal40.207371
Signal(P)203.300186
Spike_AFFX-r2-Bs-phe_3-5-ratio2.005419
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7182,Count:9
Spike_AFFX-r2-P1-cre_5_signal1870.572998
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7130
Signal(M)13.098406
BackgroundAvg:78.33,Std:0.86,Min:76.3,Max:81.0
Spike_AFFX-r2-Ec-bioC_avg-signal148.459229
Spike_AFFX-r2-Bs-dap_avg-signal77.966988
Spike_AFFX-r2-Bs-dap_3-5-ratio5.181581
Spike_AFFX-r2-Ec-bioB_5_signal33.475792
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.346111
NF1.000000
HZ4
Tau0.015000

Slide: Scofield_592-9_Mock-induced_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 ("Scofield_592-9_Mock-induced_Rep3_ATH1") was made from "" 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: Scofield_592-9_Mock-induced_Rep3_ATH1
Organism:
Stock Code:
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:0.362976
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-ratio1.191675
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.234179
Spike_AFFX-r2-Bs-dap_5_signal35.960537
NoiseAvg:2.93,Std:0.06,Min:2.7,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.143610
#P15182
Spike_AFFX-r2-Bs-phe_M_signal17.178905
Corner-Avg:8832,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal85.598793
Spike_AFFX-r2-Ec-bioB_3_signal70.227150
Spike_AFFX-r2-Bs-lys_M_signal11.024907
Spike_AFFX-r2-P1-cre_3_signal3437.740234
Spike_AFFX-r2-Bs-lys_3-5-ratio2.267408
Spike_AFFX-r2-Bs-dap_M_signal128.523727
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.979092
Spike_AFFX-r2-Ec-bioB_avg-signal70.909279
Spike_AFFX-r2-Bs-thr_avg-signal35.487377
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal665.043152
Spike_AFFX-r2-Bs-phe_5_signal25.561617
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1036.472168
RawQ2.677941
Spike_AFFX-r2-Bs-lys_5_signal13.213681
Signal(A)2.739705
%A32.029812
Signal(All)140.802002
Corner+Avg:142,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal276.939911
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal29.669884
Spike_AFFX-r2-Ec-bioD_avg-signal850.757690
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.558525
Spike_AFFX-r2-Bs-lys_avg-signal18.066465
Spike_AFFX-r2-P1-cre_avg-signal3161.268555
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.411662
Spike_AFFX-r2-Bs-thr_3_signal48.093292
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-signal24.136803
Spike_AFFX-r2-Bs-dap_3_signal169.654068
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.558504
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal239.223618
#M322
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal29.960806
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.157661
Spike_AFFX-r2-Bs-thr_M_signal42.225235
Signal(P)209.976730
Spike_AFFX-r2-Bs-phe_3-5-ratio1.160720
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6785,Count:9
Spike_AFFX-r2-P1-cre_5_signal2884.797119
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7306
Signal(M)11.834590
BackgroundAvg:60.41,Std:0.35,Min:59.7,Max:61.7
Spike_AFFX-r2-Ec-bioC_avg-signal258.081757
Spike_AFFX-r2-Bs-dap_avg-signal111.379448
Spike_AFFX-r2-Bs-dap_3-5-ratio4.717784
Spike_AFFX-r2-Ec-bioB_5_signal56.901894
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.362976
NF1.000000
HZ4
Tau0.015000

Slide: Scofield_592-10_DEX-induced_Rep3_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 ("Scofield_592-10_DEX-induced_Rep3_ATH1") was made from "" 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: Scofield_592-10_DEX-induced_Rep3_ATH1
Organism:
Stock Code:
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:0.50009
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-ratio1.001167
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.939128
Spike_AFFX-r2-Bs-dap_5_signal58.205208
NoiseAvg:2.99,Std:0.10,Min:2.7,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.296747
#P14800
Spike_AFFX-r2-Bs-phe_M_signal26.633358
Corner-Avg:8102,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal68.648170
Spike_AFFX-r2-Ec-bioB_3_signal56.535088
Spike_AFFX-r2-Bs-lys_M_signal9.134779
Spike_AFFX-r2-P1-cre_3_signal2773.092285
Spike_AFFX-r2-Bs-lys_3-5-ratio1.914653
Spike_AFFX-r2-Bs-dap_M_signal168.674393
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.672314
Spike_AFFX-r2-Ec-bioB_avg-signal61.794270
Spike_AFFX-r2-Bs-thr_avg-signal67.605217
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal467.927826
Spike_AFFX-r2-Bs-phe_5_signal46.734604
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal931.752014
RawQ2.833298
Spike_AFFX-r2-Bs-lys_5_signal20.822430
Signal(A)3.707778
%A33.419552
Signal(All)141.397125
Corner+Avg:125,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal247.286880
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal46.190933
Spike_AFFX-r2-Ec-bioD_avg-signal699.839905
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.883820
Spike_AFFX-r2-Bs-lys_avg-signal23.274984
Spike_AFFX-r2-P1-cre_avg-signal2771.475586
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.696624
Spike_AFFX-r2-Bs-thr_3_signal94.832771
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-signal39.852966
Spike_AFFX-r2-Bs-dap_3_signal257.967865
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.991230
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal203.748001
#M387
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal39.867737
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.213690
Spike_AFFX-r2-Bs-thr_M_signal87.686127
Signal(P)215.670654
Spike_AFFX-r2-Bs-phe_3-5-ratio0.988367
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6778,Count:9
Spike_AFFX-r2-P1-cre_5_signal2769.858643
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7623
Signal(M)13.122247
BackgroundAvg:66.27,Std:0.39,Min:65.5,Max:67.6
Spike_AFFX-r2-Ec-bioC_avg-signal225.517441
Spike_AFFX-r2-Bs-dap_avg-signal161.615829
Spike_AFFX-r2-Bs-dap_3-5-ratio4.432041
Spike_AFFX-r2-Ec-bioB_5_signal60.199554
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.500090
NF1.000000
HZ4
Tau0.015000

Slide: Scofield_592-11_CHX-treated_Rep3_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 ("Scofield_592-11_CHX-treated_Rep3_ATH1") was made from "" 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: Scofield_592-11_CHX-treated_Rep3_ATH1
Organism:
Stock Code:
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:0.786522
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-ratio1.322579
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.148330
Spike_AFFX-r2-Bs-dap_5_signal21.663410
NoiseAvg:2.64,Std:0.08,Min:2.4,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal13.107971
#P14674
Spike_AFFX-r2-Bs-phe_M_signal11.076286
Corner-Avg:5875,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal75.757629
Spike_AFFX-r2-Ec-bioB_3_signal63.261677
Spike_AFFX-r2-Bs-lys_M_signal15.388321
Spike_AFFX-r2-P1-cre_3_signal3474.835205
Spike_AFFX-r2-Bs-lys_3-5-ratio3.176521
Spike_AFFX-r2-Bs-dap_M_signal73.546852
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.409594
Spike_AFFX-r2-Ec-bioB_avg-signal64.703148
Spike_AFFX-r2-Bs-thr_avg-signal40.919579
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal577.667053
Spike_AFFX-r2-Bs-phe_5_signal20.312647
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal910.534851
RawQ2.627511
Spike_AFFX-r2-Bs-lys_5_signal12.151840
Signal(A)4.692911
%A33.783428
Signal(All)145.596298
Corner+Avg:92,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal263.660034
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal13.069145
Spike_AFFX-r2-Ec-bioD_avg-signal744.100952
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.331436
Spike_AFFX-r2-Bs-lys_avg-signal22.046913
Spike_AFFX-r2-P1-cre_avg-signal3051.076660
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.885138
Spike_AFFX-r2-Bs-thr_3_signal70.908798
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-signal14.819359
Spike_AFFX-r2-Bs-dap_3_signal94.501053
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.576228
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal252.648819
#M430
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal38.600578
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.043583
Spike_AFFX-r2-Bs-thr_M_signal38.741966
Signal(P)223.339310
Spike_AFFX-r2-Bs-phe_3-5-ratio0.643399
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4242,Count:9
Spike_AFFX-r2-P1-cre_5_signal2627.318359
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7706
Signal(M)17.690676
BackgroundAvg:63.46,Std:0.55,Min:62.1,Max:64.9
Spike_AFFX-r2-Ec-bioC_avg-signal258.154419
Spike_AFFX-r2-Bs-dap_avg-signal63.237106
Spike_AFFX-r2-Bs-dap_3-5-ratio4.362243
Spike_AFFX-r2-Ec-bioB_5_signal55.090153
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.786522
NF1.000000
HZ4
Tau0.015000

Slide: Scofield_592-12_CHX+DEX-induced_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 ("Scofield_592-12_CHX+DEX-induced_Rep3_ATH1") was made from "" 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: Scofield_592-12_CHX+DEX-induced_Rep3_ATH1
Organism:
Stock Code:
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:0.717951
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-ratio1.074723
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.785786
Spike_AFFX-r2-Bs-dap_5_signal14.000978
NoiseAvg:2.83,Std:0.08,Min:2.6,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal17.906067
#P14402
Spike_AFFX-r2-Bs-phe_M_signal9.464609
Corner-Avg:5365,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal71.345680
Spike_AFFX-r2-Ec-bioB_3_signal52.973351
Spike_AFFX-r2-Bs-lys_M_signal9.048818
Spike_AFFX-r2-P1-cre_3_signal3560.747070
Spike_AFFX-r2-Bs-lys_3-5-ratio2.469980
Spike_AFFX-r2-Bs-dap_M_signal40.294476
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.735660
Spike_AFFX-r2-Ec-bioB_avg-signal63.911163
Spike_AFFX-r2-Bs-thr_avg-signal36.913807
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal601.837341
Spike_AFFX-r2-Bs-phe_5_signal15.191726
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1031.122803
RawQ2.729725
Spike_AFFX-r2-Bs-lys_5_signal9.907248
Signal(A)5.383448
%A35.054802
Signal(All)145.452057
Corner+Avg:89,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal289.783020
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal8.544588
Spike_AFFX-r2-Ec-bioD_avg-signal816.480103
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.138973
Spike_AFFX-r2-Bs-lys_avg-signal14.475591
Spike_AFFX-r2-P1-cre_avg-signal3436.961914
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.806225
Spike_AFFX-r2-Bs-thr_3_signal48.984913
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal11.066975
Spike_AFFX-r2-Bs-dap_3_signal85.744278
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.713292
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal246.787994
#M412
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.470707
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.174218
Spike_AFFX-r2-Bs-thr_M_signal43.850437
Signal(P)226.811752
Spike_AFFX-r2-Bs-phe_3-5-ratio0.562450
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:3671,Count:9
Spike_AFFX-r2-P1-cre_5_signal3313.176758
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7996
Signal(M)19.836706
BackgroundAvg:65.61,Std:0.42,Min:64.5,Max:66.9
Spike_AFFX-r2-Ec-bioC_avg-signal268.285522
Spike_AFFX-r2-Bs-dap_avg-signal46.679913
Spike_AFFX-r2-Bs-dap_3-5-ratio6.124163
Spike_AFFX-r2-Ec-bioB_5_signal67.414452
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.717951
NF1.000000
HZ4
Tau0.015000


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