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Experiment: Transcriptomic analysis of inducible RNAi transgenic plants

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-622

The objective of this experiment is to proof the concept of tetrapyrrole-mediated signaling by analysis of the primary response on nuclear transcription by using an inducible transgene expression system. Transgenic plants with chemical induced silencing (RNAi) of genes encoding enzymes of the Mg branch (chlH, chlM, chl27) will allow us to explore time-resolved early variations of nuclear gene expression upon induced changes of activities of these specific steps in the chlorophyll-synthesizing branch of tetrapyrrole biosynthesis.For transcriptome analysis we used green tissue of three weeks old arabidopsis seedlings treated with dexamethasone for 24 h. The seedlings were grown in little pots on soil under the same conditions.

About the Experimenter

Name: Annabel Salinas Hartwig
Head of Lab Name: Bernhard Grimm
Lab:
Address:Department of Plant Physiology, Institute of Biology, Faculty of Mathematics and Natural Sciences I, Humboldt-University zu Berlin
Philippstrasse 13, Haus 12, Unter den Linden 6, Berlin, Berlin, 10099, GERMANY
Postcode: 10099
Country: GERMANY
 
Telephone Number: +493020936102
Fax Number: +493020936337

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: induced_mutation
Number of Slides:8
 
Experimental Parameters:
parameterinduced_mutation
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Salinas Hartwig: Transcriptomic analysis of inducible RNAi transgenic plants

Slide: Salinas-Hartwig_622-1_Col-0_Rep1_ATH1

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Salinas-Hartwig_622-1_Col-0_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: Salinas-Hartwig_622-1_Col-0_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:0.60605
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-ratio1.437595
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.375932
Spike_AFFX-r2-Bs-dap_5_signal34.408134
NoiseAvg:3.00,Std:0.09,Min:2.8,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_signal9.217803
#P14008
Spike_AFFX-r2-Bs-phe_M_signal37.277489
Corner-Avg:13847,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal13.639519
Spike_AFFX-r2-Ec-bioB_3_signal18.089132
Spike_AFFX-r2-Bs-lys_M_signal23.059793
Spike_AFFX-r2-P1-cre_3_signal5260.124023
Spike_AFFX-r2-Bs-lys_3-5-ratio2.343039
Spike_AFFX-r2-Bs-dap_M_signal177.819885
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.880625
Spike_AFFX-r2-Ec-bioB_avg-signal14.958489
Spike_AFFX-r2-Bs-thr_avg-signal49.605816
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1101.849243
Spike_AFFX-r2-Bs-phe_5_signal25.138798
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1445.770264
RawQ2.591945
Spike_AFFX-r2-Bs-lys_5_signal21.252481
Signal(A)5.578632
%A36.505917
Signal(All)150.343277
Corner+Avg:233,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal271.815887
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal76.267235
Spike_AFFX-r2-Ec-bioD_avg-signal1273.809814
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.411663
Spike_AFFX-r2-Bs-lys_avg-signal31.369219
Spike_AFFX-r2-P1-cre_avg-signal4459.548828
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.082420
Spike_AFFX-r2-Bs-thr_3_signal100.295456
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-signal46.227840
Spike_AFFX-r2-Bs-dap_3_signal361.884644
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.312131
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal271.911163
#M475
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal49.795387
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.999650
Spike_AFFX-r2-Bs-thr_M_signal39.304188
Signal(P)240.828659
Spike_AFFX-r2-Bs-phe_3-5-ratio3.033846
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12661,Count:9
Spike_AFFX-r2-P1-cre_5_signal3658.973633
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8327
Signal(M)19.682667
BackgroundAvg:61.24,Std:0.90,Min:58.9,Max:63.2
Spike_AFFX-r2-Ec-bioC_avg-signal271.863525
Spike_AFFX-r2-Bs-dap_avg-signal191.370895
Spike_AFFX-r2-Bs-dap_3-5-ratio10.517415
Spike_AFFX-r2-Ec-bioB_5_signal13.146817
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.606050
NF1.000000
HZ4
Tau0.015000

Slide: Salinas-Hartwig_622-2_Col-0_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 ("Salinas-Hartwig_622-2_Col-0_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: Salinas-Hartwig_622-2_Col-0_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:0.484578
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-ratio1.370960
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.255326
Spike_AFFX-r2-Bs-dap_5_signal26.546427
NoiseAvg:3.25,Std:0.12,Min:2.9,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionM
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.203791
#P14585
Spike_AFFX-r2-Bs-phe_M_signal31.220665
Corner-Avg:13764,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal11.628036
Spike_AFFX-r2-Ec-bioB_3_signal16.509098
Spike_AFFX-r2-Bs-lys_M_signal16.764887
Spike_AFFX-r2-P1-cre_3_signal4493.170898
Spike_AFFX-r2-Bs-lys_3-5-ratio3.175108
Spike_AFFX-r2-Bs-dap_M_signal155.222748
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.610313
Spike_AFFX-r2-Ec-bioB_avg-signal13.762792
Spike_AFFX-r2-Bs-thr_avg-signal40.257439
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal981.675293
Spike_AFFX-r2-Bs-phe_5_signal21.183289
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1375.374390
RawQ2.747273
Spike_AFFX-r2-Bs-lys_5_signal15.811355
Signal(A)4.557074
%A34.160458
Signal(All)144.971664
Corner+Avg:277,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal250.844376
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal65.413345
Spike_AFFX-r2-Ec-bioD_avg-signal1178.524902
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.941254
Spike_AFFX-r2-Bs-lys_avg-signal27.593002
Spike_AFFX-r2-P1-cre_avg-signal3885.281250
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.898290
Spike_AFFX-r2-Bs-thr_3_signal77.654045
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-signal39.272434
Spike_AFFX-r2-Bs-dap_3_signal332.683807
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.401048
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal258.582275
#M433
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal50.202763
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.970076
Spike_AFFX-r2-Bs-thr_M_signal32.914486
Signal(P)223.730103
Spike_AFFX-r2-Bs-phe_3-5-ratio3.087969
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12758,Count:9
Spike_AFFX-r2-P1-cre_5_signal3277.391357
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7792
Signal(M)18.918127
BackgroundAvg:63.46,Std:0.70,Min:61.5,Max:65.7
Spike_AFFX-r2-Ec-bioC_avg-signal254.713318
Spike_AFFX-r2-Bs-dap_avg-signal171.484329
Spike_AFFX-r2-Bs-dap_3-5-ratio12.532150
Spike_AFFX-r2-Ec-bioB_5_signal13.151239
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.484578
NF1.000000
HZ4
Tau0.015000

Slide: Salinas-Hartwig_622-3_ChlH-RNAi_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 ("Salinas-Hartwig_622-3_ChlH-RNAi_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: Salinas-Hartwig_622-3_ChlH-RNAi_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:0.557004
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-ratio1.362795
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.923667
Spike_AFFX-r2-Bs-dap_5_signal51.156406
NoiseAvg:2.95,Std:0.06,Min:2.7,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionM
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.183379
#P14396
Spike_AFFX-r2-Bs-phe_M_signal44.971748
Corner-Avg:14159,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal14.491055
Spike_AFFX-r2-Ec-bioB_3_signal12.711047
Spike_AFFX-r2-Bs-lys_M_signal17.212196
Spike_AFFX-r2-P1-cre_3_signal5172.971680
Spike_AFFX-r2-Bs-lys_3-5-ratio1.578115
Spike_AFFX-r2-Bs-dap_M_signal266.108337
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.941429
Spike_AFFX-r2-Ec-bioB_avg-signal13.654537
Spike_AFFX-r2-Bs-thr_avg-signal62.473724
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1158.426514
Spike_AFFX-r2-Bs-phe_5_signal39.476719
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1650.101563
RawQ2.621482
Spike_AFFX-r2-Bs-lys_5_signal36.084869
Signal(A)4.556849
%A35.142483
Signal(All)147.027756
Corner+Avg:238,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal311.775238
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal93.470093
Spike_AFFX-r2-Ec-bioD_avg-signal1404.264038
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.112671
Spike_AFFX-r2-Bs-lys_avg-signal36.747715
Spike_AFFX-r2-P1-cre_avg-signal4484.413086
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.744849
Spike_AFFX-r2-Bs-thr_3_signal122.362152
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-signal59.306183
Spike_AFFX-r2-Bs-dap_3_signal532.609802
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.424433
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal326.463623
#M398
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal56.946083
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.955008
Spike_AFFX-r2-Bs-thr_M_signal53.875648
Signal(P)229.939896
Spike_AFFX-r2-Bs-phe_3-5-ratio2.367727
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12506,Count:9
Spike_AFFX-r2-P1-cre_5_signal3795.854736
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8016
Signal(M)17.488726
BackgroundAvg:61.18,Std:0.25,Min:60.3,Max:61.8
Spike_AFFX-r2-Ec-bioC_avg-signal319.119446
Spike_AFFX-r2-Bs-dap_avg-signal283.291534
Spike_AFFX-r2-Bs-dap_3-5-ratio10.411400
Spike_AFFX-r2-Ec-bioB_5_signal13.761510
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.557004
NF1.000000
HZ4
Tau0.015000

Slide: Salinas-Hartwig_622-4_ChlH-RNAi_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 ("Salinas-Hartwig_622-4_ChlH-RNAi_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: Salinas-Hartwig_622-4_ChlH-RNAi_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:0.467933
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-ratio1.237989
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.493758
Spike_AFFX-r2-Bs-dap_5_signal37.915371
NoiseAvg:3.26,Std:0.13,Min:3.0,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_signal3.832381
#P14632
Spike_AFFX-r2-Bs-phe_M_signal40.402294
Corner-Avg:15481,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal18.289894
Spike_AFFX-r2-Ec-bioB_3_signal20.793125
Spike_AFFX-r2-Bs-lys_M_signal19.730848
Spike_AFFX-r2-P1-cre_3_signal4621.798828
Spike_AFFX-r2-Bs-lys_3-5-ratio2.036660
Spike_AFFX-r2-Bs-dap_M_signal184.929794
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio28.018393
Spike_AFFX-r2-Ec-bioB_avg-signal17.667677
Spike_AFFX-r2-Bs-thr_avg-signal52.776871
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1140.328003
Spike_AFFX-r2-Bs-phe_5_signal24.180016
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1680.685181
RawQ2.803380
Spike_AFFX-r2-Bs-lys_5_signal26.499102
Signal(A)3.931889
%A34.370892
Signal(All)145.918625
Corner+Avg:270,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal306.896973
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal61.013302
Spike_AFFX-r2-Ec-bioD_avg-signal1410.506592
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.147301
Spike_AFFX-r2-Bs-lys_avg-signal33.399868
Spike_AFFX-r2-P1-cre_avg-signal4177.555176
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.481806
Spike_AFFX-r2-Bs-thr_3_signal107.377144
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-signal41.865204
Spike_AFFX-r2-Bs-dap_3_signal377.516479
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.473861
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal293.420074
#M338
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal53.969658
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.045930
Spike_AFFX-r2-Bs-thr_M_signal47.121078
Signal(P)224.980850
Spike_AFFX-r2-Bs-phe_3-5-ratio2.523294
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13445,Count:9
Spike_AFFX-r2-P1-cre_5_signal3733.311523
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7840
Signal(M)16.739965
BackgroundAvg:67.29,Std:0.99,Min:65.1,Max:69.5
Spike_AFFX-r2-Ec-bioC_avg-signal300.158508
Spike_AFFX-r2-Bs-dap_avg-signal200.120544
Spike_AFFX-r2-Bs-dap_3-5-ratio9.956819
Spike_AFFX-r2-Ec-bioB_5_signal13.920012
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.467933
NF1.000000
HZ4
Tau0.015000

Slide: Salinas-Hartwig_622-5_ChlM-RNAi _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 ("Salinas-Hartwig_622-5_ChlM-RNAi _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: Salinas-Hartwig_622-5_ChlM-RNAi _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:0.393776
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-ratio1.361020
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.067453
Spike_AFFX-r2-Bs-dap_5_signal41.431629
NoiseAvg:3.89,Std:0.10,Min:3.7,Max:4.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionM
Spike_AFFX-r2-Bs-thr_5_signal7.775263
#P14557
Spike_AFFX-r2-Bs-phe_M_signal37.336895
Corner-Avg:16163,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal13.837987
Spike_AFFX-r2-Ec-bioB_3_signal12.669920
Spike_AFFX-r2-Bs-lys_M_signal23.796881
Spike_AFFX-r2-P1-cre_3_signal3859.104004
Spike_AFFX-r2-Bs-lys_3-5-ratio2.183794
Spike_AFFX-r2-Bs-dap_M_signal189.628250
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio13.971437
Spike_AFFX-r2-Ec-bioB_avg-signal12.792404
Spike_AFFX-r2-Bs-thr_avg-signal52.451542
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal906.092773
Spike_AFFX-r2-Bs-phe_5_signal27.145981
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1303.881226
RawQ3.067846
Spike_AFFX-r2-Bs-lys_5_signal28.089163
Signal(A)4.309440
%A34.313896
Signal(All)143.031021
Corner+Avg:288,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal237.269958
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal78.377884
Spike_AFFX-r2-Ec-bioD_avg-signal1104.987061
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.818501
Spike_AFFX-r2-Bs-lys_avg-signal37.742329
Spike_AFFX-r2-P1-cre_avg-signal3347.276367
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.867602
Spike_AFFX-r2-Bs-thr_3_signal108.631599
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-signal47.620255
Spike_AFFX-r2-Bs-dap_3_signal412.026459
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.439015
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal233.966675
#M426
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal61.340946
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.014119
Spike_AFFX-r2-Bs-thr_M_signal40.947758
Signal(P)221.310501
Spike_AFFX-r2-Bs-phe_3-5-ratio2.887274
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14457,Count:9
Spike_AFFX-r2-P1-cre_5_signal2835.448975
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7827
Signal(M)16.879719
BackgroundAvg:81.78,Std:0.49,Min:79.5,Max:82.6
Spike_AFFX-r2-Ec-bioC_avg-signal235.618317
Spike_AFFX-r2-Bs-dap_avg-signal214.362122
Spike_AFFX-r2-Bs-dap_3-5-ratio9.944733
Spike_AFFX-r2-Ec-bioB_5_signal11.869304
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.393776
NF1.000000
HZ4
Tau0.015000

Slide: Salinas-Hartwig_622-6_ChlM-RNAi _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 ("Salinas-Hartwig_622-6_ChlM-RNAi _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: Salinas-Hartwig_622-6_ChlM-RNAi _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:0.43136
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-ratio1.314555
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.814748
Spike_AFFX-r2-Bs-dap_5_signal40.198898
NoiseAvg:3.63,Std:0.10,Min:3.3,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.131586
#P14501
Spike_AFFX-r2-Bs-phe_M_signal42.020439
Corner-Avg:15004,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal17.610924
Spike_AFFX-r2-Ec-bioB_3_signal10.575171
Spike_AFFX-r2-Bs-lys_M_signal19.211586
Spike_AFFX-r2-P1-cre_3_signal4065.887695
Spike_AFFX-r2-Bs-lys_3-5-ratio1.941596
Spike_AFFX-r2-Bs-dap_M_signal184.845337
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.080364
Spike_AFFX-r2-Ec-bioB_avg-signal13.721924
Spike_AFFX-r2-Bs-thr_avg-signal42.441383
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal906.396912
Spike_AFFX-r2-Bs-phe_5_signal30.224621
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1265.789673
RawQ3.017921
Spike_AFFX-r2-Bs-lys_5_signal24.423429
Signal(A)4.676469
%A34.436649
Signal(All)143.021042
Corner+Avg:261,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal257.998993
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal71.795959
Spike_AFFX-r2-Ec-bioD_avg-signal1086.093262
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.572994
Spike_AFFX-r2-Bs-lys_avg-signal30.351816
Spike_AFFX-r2-P1-cre_avg-signal3579.431641
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.990355
Spike_AFFX-r2-Bs-thr_3_signal81.866905
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-signal48.013672
Spike_AFFX-r2-Bs-dap_3_signal367.289185
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.396507
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal246.836365
#M454
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal47.420429
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.045223
Spike_AFFX-r2-Bs-thr_M_signal35.325657
Signal(P)221.881989
Spike_AFFX-r2-Bs-phe_3-5-ratio2.375413
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14101,Count:9
Spike_AFFX-r2-P1-cre_5_signal3092.975586
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7855
Signal(M)17.765493
BackgroundAvg:74.59,Std:0.71,Min:72.9,Max:76.0
Spike_AFFX-r2-Ec-bioC_avg-signal252.417679
Spike_AFFX-r2-Bs-dap_avg-signal197.444473
Spike_AFFX-r2-Bs-dap_3-5-ratio9.136797
Spike_AFFX-r2-Ec-bioB_5_signal12.979678
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.431360
NF1.000000
HZ4
Tau0.015000

Slide: Salinas-Hartwig_622-7_Chl27-RNAi_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 ("Salinas-Hartwig_622-7_Chl27-RNAi_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: Salinas-Hartwig_622-7_Chl27-RNAi_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:0.451183
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-ratio1.348418
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.494853
Spike_AFFX-r2-Bs-dap_5_signal23.984457
NoiseAvg:3.59,Std:0.13,Min:3.0,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.835073
#P14260
Spike_AFFX-r2-Bs-phe_M_signal33.464802
Corner-Avg:15201,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal17.999386
Spike_AFFX-r2-Ec-bioB_3_signal18.459675
Spike_AFFX-r2-Bs-lys_M_signal17.157385
Spike_AFFX-r2-P1-cre_3_signal4030.876709
Spike_AFFX-r2-Bs-lys_3-5-ratio2.630776
Spike_AFFX-r2-Bs-dap_M_signal156.172897
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.376934
Spike_AFFX-r2-Ec-bioB_avg-signal16.269295
Spike_AFFX-r2-Bs-thr_avg-signal39.927219
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal933.804993
Spike_AFFX-r2-Bs-phe_5_signal25.251701
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1399.031860
RawQ2.930585
Spike_AFFX-r2-Bs-lys_5_signal19.859768
Signal(A)4.928176
%A35.708023
Signal(All)145.941757
Corner+Avg:265,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal220.242355
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal53.474796
Spike_AFFX-r2-Ec-bioD_avg-signal1166.418457
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.516441
Spike_AFFX-r2-Bs-lys_avg-signal29.754583
Spike_AFFX-r2-P1-cre_avg-signal3510.107178
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.775537
Spike_AFFX-r2-Bs-thr_3_signal69.094551
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-signal37.397099
Spike_AFFX-r2-Bs-dap_3_signal351.131439
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.498206
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal237.839951
#M405
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal52.246593
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.926011
Spike_AFFX-r2-Bs-thr_M_signal39.852032
Signal(P)230.135818
Spike_AFFX-r2-Bs-phe_3-5-ratio2.117671
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13840,Count:9
Spike_AFFX-r2-P1-cre_5_signal2989.337646
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8145
Signal(M)17.418688
BackgroundAvg:69.84,Std:0.70,Min:68.1,Max:71.4
Spike_AFFX-r2-Ec-bioC_avg-signal229.041153
Spike_AFFX-r2-Bs-dap_avg-signal177.096252
Spike_AFFX-r2-Bs-dap_3-5-ratio14.639957
Spike_AFFX-r2-Ec-bioB_5_signal12.348825
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.451183
NF1.000000
HZ4
Tau0.015000

Slide: Salinas-Hartwig_622-8_Chl27-RNAi_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 ("Salinas-Hartwig_622-8_Chl27-RNAi_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: Salinas-Hartwig_622-8_Chl27-RNAi_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:0.575344
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-ratio1.388134
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.166674
Spike_AFFX-r2-Bs-dap_5_signal38.812298
NoiseAvg:3.23,Std:0.08,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_signal10.324468
#P14046
Spike_AFFX-r2-Bs-phe_M_signal41.648079
Corner-Avg:17453,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal14.771397
Spike_AFFX-r2-Ec-bioB_3_signal18.483612
Spike_AFFX-r2-Bs-lys_M_signal24.571064
Spike_AFFX-r2-P1-cre_3_signal5440.448242
Spike_AFFX-r2-Bs-lys_3-5-ratio2.702270
Spike_AFFX-r2-Bs-dap_M_signal193.202042
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.157778
Spike_AFFX-r2-Ec-bioB_avg-signal16.366003
Spike_AFFX-r2-Bs-thr_avg-signal46.959034
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1349.226563
Spike_AFFX-r2-Bs-phe_5_signal28.752092
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1869.275269
RawQ2.604600
Spike_AFFX-r2-Bs-lys_5_signal20.528852
Signal(A)5.645704
%A36.711967
Signal(All)148.896820
Corner+Avg:292,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal279.917847
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal61.362316
Spike_AFFX-r2-Ec-bioD_avg-signal1609.250977
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.578255
Spike_AFFX-r2-Bs-lys_avg-signal33.524807
Spike_AFFX-r2-P1-cre_avg-signal4679.851074
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.709776
Spike_AFFX-r2-Bs-thr_3_signal84.224709
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-signal43.920826
Spike_AFFX-r2-Bs-dap_3_signal381.755402
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.385442
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal313.734192
#M390
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal55.474499
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.892213
Spike_AFFX-r2-Bs-thr_M_signal46.327942
Signal(P)237.834473
Spike_AFFX-r2-Bs-phe_3-5-ratio2.134186
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14673,Count:9
Spike_AFFX-r2-P1-cre_5_signal3919.253662
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8374
Signal(M)21.631334
BackgroundAvg:63.46,Std:0.29,Min:62.5,Max:64.4
Spike_AFFX-r2-Ec-bioC_avg-signal296.826019
Spike_AFFX-r2-Bs-dap_avg-signal204.589920
Spike_AFFX-r2-Bs-dap_3-5-ratio9.835939
Spike_AFFX-r2-Ec-bioB_5_signal15.843000
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.575344
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team