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Experiment: ERFVII and hypoxia

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-588

The aim of this analysis is to compare plants with increased expression of At1g53910 and decreased expression of At1g53910 and At3g14230 in their response to hypoxia (1% O2). HA-tagged overexpressors of At1g53910 and knock-out lines obtained by overexpression of an artificial microRNA against At1g53910 and At3g14230 were used. Plants were treated for 90 mins under hypoxic or normoxic conditions and then the above-ground tissues were collected and rapidly frozen in liquid nitrogen. RNA was extracted using the RNeasy (Qiagen) extraction kit.Control wt are also used to test differentially regulated genes in plants overexpressing an HA tagged version of At5g21960.

About the Experimenter

Name:Mr Francesco Licausi
Head of Lab Name:Dr Joost van Dongen
Lab:
Institute: Department 1: Molecular Physiology
Address:Max-Planck-Institut fur Molekulare Pflanzenphysiologie
Wissenschaftspark Golm, Am Muhlenberg 1, Potsdam, Golm, Brandenburg
Postcode: 14476
Country: GERMANY
 
Telephone Number: +49 0331 567 8353

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

About this Experiment

Experiment Type: genetic_modification_design, stimulus_or_stress_design
Number of Slides:20
 
Experimental Parameters:
parameterchange_oxygen_concentration
parametergenetic_modification
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Licausi: ERFVII and hypoxia

Slide: Licausi_588-1_WT_Control_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 ("Licausi_588-1_WT_Control_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-1_WT_Control_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
in vivo Treatment: Plants treated for 90 min in the dark at normoxic conditions (21% O2).
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:0.342688
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-ratio1.299812
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.134980
Spike_AFFX-r2-Bs-dap_5_signal35.935242
NoiseAvg:3.11,Std:0.08,Min:2.9,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal14.932344
#P14452
Spike_AFFX-r2-Bs-phe_M_signal23.362188
Corner-Avg:11096,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal92.168953
Spike_AFFX-r2-Ec-bioB_3_signal69.573631
Spike_AFFX-r2-Bs-lys_M_signal9.764972
Spike_AFFX-r2-P1-cre_3_signal3463.089844
Spike_AFFX-r2-Bs-lys_3-5-ratio1.859316
Spike_AFFX-r2-Bs-dap_M_signal123.382988
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.649010
Spike_AFFX-r2-Ec-bioB_avg-signal74.347343
Spike_AFFX-r2-Bs-thr_avg-signal36.060184
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal679.658264
Spike_AFFX-r2-Bs-phe_5_signal20.387222
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1118.453003
RawQ2.851311
Spike_AFFX-r2-Bs-lys_5_signal11.388805
Signal(A)2.706595
%A35.089874
Signal(All)141.635788
Corner+Avg:188,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal239.450012
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal16.872904
Spike_AFFX-r2-Ec-bioD_avg-signal899.055664
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.358177
Spike_AFFX-r2-Bs-lys_avg-signal14.109722
Spike_AFFX-r2-P1-cre_avg-signal3063.694824
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.551951
Spike_AFFX-r2-Bs-thr_3_signal54.488270
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal20.207438
Spike_AFFX-r2-Bs-dap_3_signal153.767380
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.645611
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal271.180389
#M354
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.175388
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.882992
Spike_AFFX-r2-Bs-thr_M_signal38.759945
Signal(P)221.780029
Spike_AFFX-r2-Bs-phe_3-5-ratio0.827622
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8995,Count:9
Spike_AFFX-r2-P1-cre_5_signal2664.299561
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8004
Signal(M)10.971050
BackgroundAvg:67.03,Std:0.33,Min:66.1,Max:67.9
Spike_AFFX-r2-Ec-bioC_avg-signal255.315201
Spike_AFFX-r2-Bs-dap_avg-signal104.361870
Spike_AFFX-r2-Bs-dap_3-5-ratio4.279013
Spike_AFFX-r2-Ec-bioB_5_signal61.299438
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.342688
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-2_WT_Control_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 ("Licausi_588-2_WT_Control_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-2_WT_Control_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
in vivo Treatment: Plants treated for 90 min in the dark at normoxic conditions (21% O2).
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:0.507373
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-ratio1.161436
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.098552
Spike_AFFX-r2-Bs-dap_5_signal46.725330
NoiseAvg:2.50,Std:0.04,Min:2.4,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal33.993526
#P14191
Spike_AFFX-r2-Bs-phe_M_signal31.003403
Corner-Avg:9466,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal108.567947
Spike_AFFX-r2-Ec-bioB_3_signal95.725784
Spike_AFFX-r2-Bs-lys_M_signal17.132086
Spike_AFFX-r2-P1-cre_3_signal4557.029785
Spike_AFFX-r2-Bs-lys_3-5-ratio1.730333
Spike_AFFX-r2-Bs-dap_M_signal170.484177
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.206057
Spike_AFFX-r2-Ec-bioB_avg-signal97.143959
Spike_AFFX-r2-Bs-thr_avg-signal69.562508
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal967.413391
Spike_AFFX-r2-Bs-phe_5_signal29.766001
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1527.470703
RawQ2.549795
Spike_AFFX-r2-Bs-lys_5_signal19.376318
Signal(A)3.006998
%A36.260410
Signal(All)147.622131
Corner+Avg:152,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal275.026306
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.791725
Spike_AFFX-r2-Ec-bioD_avg-signal1247.442017
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.213940
Spike_AFFX-r2-Bs-lys_avg-signal23.345299
Spike_AFFX-r2-P1-cre_avg-signal4240.323242
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.525647
Spike_AFFX-r2-Bs-thr_3_signal108.985184
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-signal29.853708
Spike_AFFX-r2-Bs-dap_3_signal219.778900
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.578922
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal414.616272
#M348
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal33.527489
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.663327
Spike_AFFX-r2-Bs-thr_M_signal65.708801
Signal(P)235.232590
Spike_AFFX-r2-Bs-phe_3-5-ratio0.967269
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7673,Count:9
Spike_AFFX-r2-P1-cre_5_signal3923.616211
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8271
Signal(M)12.081120
BackgroundAvg:58.27,Std:0.33,Min:57.4,Max:59.1
Spike_AFFX-r2-Ec-bioC_avg-signal344.821289
Spike_AFFX-r2-Bs-dap_avg-signal145.662796
Spike_AFFX-r2-Bs-dap_3-5-ratio4.703635
Spike_AFFX-r2-Ec-bioB_5_signal87.138138
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.507373
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-3_WT_Control_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 ("Licausi_588-3_WT_Control_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-3_WT_Control_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
in vivo Treatment: Plants treated for 90 min in the dark at normoxic conditions (21% O2).
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:0.582377
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-ratio1.217803
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.223215
Spike_AFFX-r2-Bs-dap_5_signal40.668858
NoiseAvg:2.42,Std:0.08,Min:2.2,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal23.105476
#P14068
Spike_AFFX-r2-Bs-phe_M_signal30.549736
Corner-Avg:9073,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal118.651344
Spike_AFFX-r2-Ec-bioB_3_signal83.962288
Spike_AFFX-r2-Bs-lys_M_signal16.134453
Spike_AFFX-r2-P1-cre_3_signal4087.252197
Spike_AFFX-r2-Bs-lys_3-5-ratio0.956987
Spike_AFFX-r2-Bs-dap_M_signal173.256805
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.687498
Spike_AFFX-r2-Ec-bioB_avg-signal90.418091
Spike_AFFX-r2-Bs-thr_avg-signal71.946739
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal849.819214
Spike_AFFX-r2-Bs-phe_5_signal36.771290
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1522.377930
RawQ2.457159
Spike_AFFX-r2-Bs-lys_5_signal28.959482
Signal(A)3.153680
%A36.681282
Signal(All)147.213211
Corner+Avg:142,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal323.134003
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal31.674097
Spike_AFFX-r2-Ec-bioD_avg-signal1186.098633
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.674706
Spike_AFFX-r2-Bs-lys_avg-signal24.269257
Spike_AFFX-r2-P1-cre_avg-signal3721.751465
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.644016
Spike_AFFX-r2-Bs-thr_3_signal131.412338
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-signal32.998371
Spike_AFFX-r2-Bs-dap_3_signal193.311111
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.791414
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal338.758331
#M375
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.713839
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.953878
Spike_AFFX-r2-Bs-thr_M_signal61.322399
Signal(P)236.502777
Spike_AFFX-r2-Bs-phe_3-5-ratio0.861381
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8659,Count:9
Spike_AFFX-r2-P1-cre_5_signal3356.250977
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8367
Signal(M)11.801105
BackgroundAvg:57.90,Std:0.51,Min:56.9,Max:59.4
Spike_AFFX-r2-Ec-bioC_avg-signal330.946167
Spike_AFFX-r2-Bs-dap_avg-signal135.745590
Spike_AFFX-r2-Bs-dap_3-5-ratio4.753296
Spike_AFFX-r2-Ec-bioB_5_signal68.640656
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.582377
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-4_WT_Hypo_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 ("Licausi_588-4_WT_Hypo_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-4_WT_Hypo_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
in vivo Treatment: Plants treated for 90 min in the dark at hypoxia conditions (1% O2).
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:0.372778
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-ratio1.209287
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.949743
Spike_AFFX-r2-Bs-dap_5_signal50.638443
NoiseAvg:2.73,Std:0.08,Min:2.5,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_signal28.273417
#P14495
Spike_AFFX-r2-Bs-phe_M_signal33.765205
Corner-Avg:10093,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal92.533272
Spike_AFFX-r2-Ec-bioB_3_signal64.084534
Spike_AFFX-r2-Bs-lys_M_signal11.368224
Spike_AFFX-r2-P1-cre_3_signal3582.287354
Spike_AFFX-r2-Bs-lys_3-5-ratio2.011961
Spike_AFFX-r2-Bs-dap_M_signal169.267929
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.390883
Spike_AFFX-r2-Ec-bioB_avg-signal74.697815
Spike_AFFX-r2-Bs-thr_avg-signal60.788849
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal702.353516
Spike_AFFX-r2-Bs-phe_5_signal32.149647
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1128.729248
RawQ2.683951
Spike_AFFX-r2-Bs-lys_5_signal19.580996
Signal(A)2.294344
%A35.054802
Signal(All)142.173584
Corner+Avg:159,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal267.854828
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.204731
Spike_AFFX-r2-Ec-bioD_avg-signal915.541382
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.546692
Spike_AFFX-r2-Bs-lys_avg-signal23.448477
Spike_AFFX-r2-P1-cre_avg-signal3272.300537
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.398509
Spike_AFFX-r2-Bs-thr_3_signal95.871841
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-signal31.373194
Spike_AFFX-r2-Bs-dap_3_signal234.147812
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.607067
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal287.925873
#M319
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal39.396206
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.930291
Spike_AFFX-r2-Bs-thr_M_signal58.221283
Signal(P)222.236328
Spike_AFFX-r2-Bs-phe_3-5-ratio0.877295
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8568,Count:9
Spike_AFFX-r2-P1-cre_5_signal2962.313721
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7996
Signal(M)10.401967
BackgroundAvg:63.48,Std:0.52,Min:61.7,Max:64.9
Spike_AFFX-r2-Ec-bioC_avg-signal277.890350
Spike_AFFX-r2-Bs-dap_avg-signal151.351395
Spike_AFFX-r2-Bs-dap_3-5-ratio4.623914
Spike_AFFX-r2-Ec-bioB_5_signal67.475639
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.372778
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-5_WT_Hypo_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 ("Licausi_588-5_WT_Hypo_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-5_WT_Hypo_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
ProtocolArabidopsis plants were grown in single pots (6 cm diameter) filled with commercial soil in a growth chamber with a photoperiod of 8h light and 16h darkness, 60% humidity during the day and 75% humidity during the night. Temperature was kept at 20°C during the light period and 16°C during the night.
Plant Spacingone plant/pot
Temperature18 °C average, 20 °C day, 16 °C night
Humidity67.5 % average, 60 % day, 75 % night
Medium
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.20
Tissue: whole plant
in vivo Treatment: Plants treated for 90 min in the dark at hypoxia conditions (1% O2).
Additional Organism Information:
Sample Descriptionhealthy green plants with 3cm diameter rosette.
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:0.41615
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-ratio1.047628
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.018081
Spike_AFFX-r2-Bs-dap_5_signal40.137398
NoiseAvg:2.71,Std:0.08,Min:2.5,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_signal24.404240
#P14290
Spike_AFFX-r2-Bs-phe_M_signal23.579000
Corner-Avg:11495,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal102.044403
Spike_AFFX-r2-Ec-bioB_3_signal80.090454
Spike_AFFX-r2-Bs-lys_M_signal9.273024
Spike_AFFX-r2-P1-cre_3_signal3770.029541
Spike_AFFX-r2-Bs-lys_3-5-ratio1.253896
Spike_AFFX-r2-Bs-dap_M_signal125.949135
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.639225
Spike_AFFX-r2-Ec-bioB_avg-signal86.934303
Spike_AFFX-r2-Bs-thr_avg-signal44.602207
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal865.412231
Spike_AFFX-r2-Bs-phe_5_signal25.512520
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1268.771973
RawQ2.561410
Spike_AFFX-r2-Bs-lys_5_signal18.966793
Signal(A)2.559534
%A35.813240
Signal(All)144.952652
Corner+Avg:190,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal329.376892
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal24.088633
Spike_AFFX-r2-Ec-bioD_avg-signal1067.092041
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.647961
Spike_AFFX-r2-Bs-lys_avg-signal17.340733
Spike_AFFX-r2-P1-cre_avg-signal3684.332031
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.538799
Spike_AFFX-r2-Bs-thr_3_signal64.408287
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-signal24.393385
Spike_AFFX-r2-Bs-dap_3_signal166.262924
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.466090
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal313.922638
#M351
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.782381
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.049230
Spike_AFFX-r2-Bs-thr_M_signal44.994102
Signal(P)229.643005
Spike_AFFX-r2-Bs-phe_3-5-ratio0.944189
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8688,Count:9
Spike_AFFX-r2-P1-cre_5_signal3598.634766
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8169
Signal(M)11.005030
BackgroundAvg:60.02,Std:0.94,Min:57.7,Max:62.7
Spike_AFFX-r2-Ec-bioC_avg-signal321.649780
Spike_AFFX-r2-Bs-dap_avg-signal110.783150
Spike_AFFX-r2-Bs-dap_3-5-ratio4.142344
Spike_AFFX-r2-Ec-bioB_5_signal78.668068
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.416150
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-6_WT_Hypo_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 ("Licausi_588-6_WT_Hypo_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-6_WT_Hypo_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
ProtocolArabidopsis plants were grown in single pots (6 cm diameter) filled with commercial soil in a growth chamber with a photoperiod of 8h light and 16h darkness, 60% humidity during the day and 75% humidity during the night. Temperature was kept at 20°C during the light period and 16°C during the night.
Plant Spacingone plant/pot
Temperature18 °C average, 20 °C day, 16 °C night
Humidity67.5 % average, 60 % day, 75 % night
Medium
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.20
Tissue: whole rosette
in vivo Treatment: Plants treated for 90 min in the dark at hypoxia conditions (1% O2).
Additional Organism Information:
Sample Descriptionhealthy green plants with 3cm diameter rosette.
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:0.525776
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-ratio0.720088
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.854026
Spike_AFFX-r2-Bs-dap_5_signal37.453217
NoiseAvg:2.70,Std:0.13,Min:2.4,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_signal18.245777
#P13898
Spike_AFFX-r2-Bs-phe_M_signal23.296566
Corner-Avg:10389,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal82.820702
Spike_AFFX-r2-Ec-bioB_3_signal61.026501
Spike_AFFX-r2-Bs-lys_M_signal8.507880
Spike_AFFX-r2-P1-cre_3_signal2819.065674
Spike_AFFX-r2-Bs-lys_3-5-ratio1.088580
Spike_AFFX-r2-Bs-dap_M_signal132.712784
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.832339
Spike_AFFX-r2-Ec-bioB_avg-signal71.768204
Spike_AFFX-r2-Bs-thr_avg-signal48.871555
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal653.864929
Spike_AFFX-r2-Bs-phe_5_signal21.851337
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1031.207031
RawQ2.594843
Spike_AFFX-r2-Bs-lys_5_signal20.915916
Signal(A)3.447514
%A37.448486
Signal(All)147.042877
Corner+Avg:164,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal261.419983
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.473127
Spike_AFFX-r2-Ec-bioD_avg-signal842.536011
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.929417
Spike_AFFX-r2-Bs-lys_avg-signal17.397482
Spike_AFFX-r2-P1-cre_avg-signal3366.979248
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.622096
Spike_AFFX-r2-Bs-thr_3_signal88.169785
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-signal22.207010
Spike_AFFX-r2-Bs-dap_3_signal145.935684
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.577095
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal261.826752
#M370
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal22.768650
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.998446
Spike_AFFX-r2-Bs-thr_M_signal40.199104
Signal(P)238.857193
Spike_AFFX-r2-Bs-phe_3-5-ratio0.982692
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8659,Count:9
Spike_AFFX-r2-P1-cre_5_signal3914.892822
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8542
Signal(M)13.410787
BackgroundAvg:59.13,Std:0.76,Min:57.4,Max:61.1
Spike_AFFX-r2-Ec-bioC_avg-signal261.623352
Spike_AFFX-r2-Bs-dap_avg-signal105.367226
Spike_AFFX-r2-Bs-dap_3-5-ratio3.896479
Spike_AFFX-r2-Ec-bioB_5_signal71.457413
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.525776
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-7_HA-RAP2.12_Control_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 ("Licausi_588-7_HA-RAP2.12_Control_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-7_HA-RAP2.12_Control_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::HA::RAP2.12
Stock Code:
Genetic Background: Col-0
Growth Conditions:
ProtocolArabidopsis plants were grown in single pots (6 cm diameter) filled with commercial soil in a growth chamber with a photoperiod of 8h light and 16h darkness, 60% humidity during the day and 75% humidity during the night. Temperature was kept at 20°C during the light period and 16°C during the night.
Plant Spacingone plant/pot
Temperature18 °C average, 20 °C day, 16 °C night
Humidity67.5 % average, 60 % day, 75 % night
Medium
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.20
Genetic Variation: T-DNA knock out mutation in At1g53910
Tissue: whole rosette
in vivo Treatment: Plants treated for 90 min in the dark at normoxic conditions (1% O2).
Additional Organism Information:
Sample Descriptionhealthy green plants with 3cm diameter rosette.
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:0.401348
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-ratio1.254553
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.135256
Spike_AFFX-r2-Bs-dap_5_signal39.183201
NoiseAvg:2.96,Std:0.05,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_signal24.503798
#P14307
Spike_AFFX-r2-Bs-phe_M_signal23.073643
Corner-Avg:11558,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal93.944702
Spike_AFFX-r2-Ec-bioB_3_signal66.010414
Spike_AFFX-r2-Bs-lys_M_signal12.459472
Spike_AFFX-r2-P1-cre_3_signal3647.994873
Spike_AFFX-r2-Bs-lys_3-5-ratio2.662454
Spike_AFFX-r2-Bs-dap_M_signal145.681854
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.067214
Spike_AFFX-r2-Ec-bioB_avg-signal72.700325
Spike_AFFX-r2-Bs-thr_avg-signal49.400913
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal782.876953
Spike_AFFX-r2-Bs-phe_5_signal19.711468
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1152.217163
RawQ2.634346
Spike_AFFX-r2-Bs-lys_5_signal15.617768
Signal(A)3.156467
%A35.690487
Signal(All)144.249512
Corner+Avg:192,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal256.378235
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal27.150438
Spike_AFFX-r2-Ec-bioD_avg-signal967.547058
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.722488
Spike_AFFX-r2-Bs-lys_avg-signal23.219610
Spike_AFFX-r2-P1-cre_avg-signal3277.899902
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.587023
Spike_AFFX-r2-Bs-thr_3_signal75.158401
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-signal23.311850
Spike_AFFX-r2-Bs-dap_3_signal166.157654
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.471773
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal266.553497
#M362
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal41.581585
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.961827
Spike_AFFX-r2-Bs-thr_M_signal48.540546
Signal(P)227.873474
Spike_AFFX-r2-Bs-phe_3-5-ratio1.377393
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8716,Count:9
Spike_AFFX-r2-P1-cre_5_signal2907.804932
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8141
Signal(M)12.289184
BackgroundAvg:61.98,Std:0.61,Min:60.5,Max:63.5
Spike_AFFX-r2-Ec-bioC_avg-signal261.465881
Spike_AFFX-r2-Bs-dap_avg-signal117.007568
Spike_AFFX-r2-Bs-dap_3-5-ratio4.240533
Spike_AFFX-r2-Ec-bioB_5_signal58.145859
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.401348
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-8_HA-RAP2.12_Control_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 ("Licausi_588-8_HA-RAP2.12_Control_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-8_HA-RAP2.12_Control_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::HA::RAP2.12
Stock Code:
Genetic Background: Col-0
Growth Conditions:
ProtocolArabidopsis plants were grown in single pots (6 cm diameter) filled with commercial soil in a growth chamber with a photoperiod of 8h light and 16h darkness, 60% humidity during the day and 75% humidity during the night. Temperature was kept at 20°C during the light period and 16°C during the night.
Plant Spacingone plant/pot
Temperature18 °C average, 20 °C day, 16 °C night
Humidity67.5 % average, 60 % day, 75 % night
Medium
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.20
Genetic Variation: T-DNA knock out mutation in At1g53910
Tissue: whole rosette
in vivo Treatment: Plants treated for 90 min in the dark at normoxic conditions (1% O2).
Additional Organism Information:
Sample Descriptionhealthy green plants with 3cm diameter rosette.
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:0.530702
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-ratio1.187093
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.001377
Spike_AFFX-r2-Bs-dap_5_signal33.168781
NoiseAvg:2.91,Std:0.08,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_signal25.824247
#P14102
Spike_AFFX-r2-Bs-phe_M_signal23.834139
Corner-Avg:9300,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal77.995316
Spike_AFFX-r2-Ec-bioB_3_signal66.141685
Spike_AFFX-r2-Bs-lys_M_signal7.331116
Spike_AFFX-r2-P1-cre_3_signal3579.158691
Spike_AFFX-r2-Bs-lys_3-5-ratio3.661784
Spike_AFFX-r2-Bs-dap_M_signal112.185333
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.409990
Spike_AFFX-r2-Ec-bioB_avg-signal70.062569
Spike_AFFX-r2-Bs-thr_avg-signal49.608959
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal626.951355
Spike_AFFX-r2-Bs-phe_5_signal26.831158
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1043.363647
RawQ2.659370
Spike_AFFX-r2-Bs-lys_5_signal9.162740
Signal(A)3.850375
%A36.584831
Signal(All)147.176544
Corner+Avg:144,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal228.742844
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal29.499851
Spike_AFFX-r2-Ec-bioD_avg-signal835.157471
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.823761
Spike_AFFX-r2-Bs-lys_avg-signal16.681942
Spike_AFFX-r2-P1-cre_avg-signal3297.110352
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.591407
Spike_AFFX-r2-Bs-thr_3_signal62.236183
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal26.721716
Spike_AFFX-r2-Bs-dap_3_signal153.808960
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.664186
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal307.426636
#M363
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal33.551971
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.744057
Spike_AFFX-r2-Bs-thr_M_signal60.766445
Signal(P)235.386627
Spike_AFFX-r2-Bs-phe_3-5-ratio1.099463
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7124,Count:9
Spike_AFFX-r2-P1-cre_5_signal3015.062256
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8345
Signal(M)15.270888
BackgroundAvg:65.51,Std:0.67,Min:63.8,Max:67.4
Spike_AFFX-r2-Ec-bioC_avg-signal268.084747
Spike_AFFX-r2-Bs-dap_avg-signal99.721031
Spike_AFFX-r2-Bs-dap_3-5-ratio4.637160
Spike_AFFX-r2-Ec-bioB_5_signal66.050713
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.530702
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-9_HA-RAP2.12_Control_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 ("Licausi_588-9_HA-RAP2.12_Control_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-9_HA-RAP2.12_Control_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::HA::RAP2.12
Stock Code:
Genetic Background: Col-0
Growth Conditions:
ProtocolArabidopsis plants were grown in single pots (6 cm diameter) filled with commercial soil in a growth chamber with a photoperiod of 8h light and 16h darkness, 60% humidity during the day and 75% humidity during the night. Temperature was kept at 20°C during the light period and 16°C during the night.
Plant Spacingone plant/pot
Temperature18 °C average, 20 °C day, 16 °C night
Humidity67.5 % average, 60 % day, 75 % night
Medium
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.20
Genetic Variation: T-DNA knock out mutation in At1g53910
Tissue: whole rosette
in vivo Treatment: Plants treated for 90 min in the dark at normoxic conditions (1% O2).
Additional Organism Information:
Sample Descriptionhealthy green plants with 3cm diameter rosette.
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:0.336518
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-ratio1.265169
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.205246
Spike_AFFX-r2-Bs-dap_5_signal42.676224
NoiseAvg:3.03,Std:0.06,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_signal21.318577
#P14727
Spike_AFFX-r2-Bs-phe_M_signal21.763933
Corner-Avg:9908,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal84.199638
Spike_AFFX-r2-Ec-bioB_3_signal60.501907
Spike_AFFX-r2-Bs-lys_M_signal7.461231
Spike_AFFX-r2-P1-cre_3_signal3191.693359
Spike_AFFX-r2-Bs-lys_3-5-ratio1.309579
Spike_AFFX-r2-Bs-dap_M_signal136.352661
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.728172
Spike_AFFX-r2-Ec-bioB_avg-signal64.966789
Spike_AFFX-r2-Bs-thr_avg-signal48.289707
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal620.800049
Spike_AFFX-r2-Bs-phe_5_signal27.928270
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal921.607910
RawQ2.714772
Spike_AFFX-r2-Bs-lys_5_signal16.438225
Signal(A)2.653538
%A34.002632
Signal(All)140.002151
Corner+Avg:167,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal240.500824
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal26.064625
Spike_AFFX-r2-Ec-bioD_avg-signal771.203979
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.563789
Spike_AFFX-r2-Bs-lys_avg-signal15.142204
Spike_AFFX-r2-P1-cre_avg-signal2857.217285
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.433582
Spike_AFFX-r2-Bs-thr_3_signal79.479324
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-signal25.252275
Spike_AFFX-r2-Bs-dap_3_signal147.189560
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.484549
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal246.746399
#M327
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.527159
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.974688
Spike_AFFX-r2-Bs-thr_M_signal44.071220
Signal(P)215.225204
Spike_AFFX-r2-Bs-phe_3-5-ratio0.933270
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7983,Count:9
Spike_AFFX-r2-P1-cre_5_signal2522.741455
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7756
Signal(M)9.929056
BackgroundAvg:64.18,Std:0.49,Min:62.4,Max:65.1
Spike_AFFX-r2-Ec-bioC_avg-signal243.623611
Spike_AFFX-r2-Bs-dap_avg-signal108.739479
Spike_AFFX-r2-Bs-dap_3-5-ratio3.448983
Spike_AFFX-r2-Ec-bioB_5_signal50.198822
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.336518
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-10_HA-RAP2.12_Hypo_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 ("Licausi_588-10_HA-RAP2.12_Hypo_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-10_HA-RAP2.12_Hypo_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::HA::RAP2.12
Stock Code:
Genetic Background: Col-0
Growth Conditions:
ProtocolArabidopsis plants were grown in single pots (6 cm diameter) filled with commercial soil in a growth chamber with a photoperiod of 8h light and 16h darkness, 60% humidity during the day and 75% humidity during the night. Temperature was kept at 20°C during the light period and 16°C during the night.
Plant Spacingone plant/pot
Temperature18 °C average, 20 °C day, 16 °C night
Humidity67.5 % average, 60 % day, 75 % night
Medium
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.20
Genetic Variation: T-DNA knock out mutation in At1g53910
Tissue: whole rosette
in vivo Treatment: Plants treated for 90 min in the dark at hypoxic conditions (21% O2).
Additional Organism Information:
Sample Descriptionhealthy green plants with 3cm diameter rosette.
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:0.324104
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-ratio1.120823
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.036296
Spike_AFFX-r2-Bs-dap_5_signal32.024151
NoiseAvg:3.07,Std:0.11,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_signal17.967951
#P14523
Spike_AFFX-r2-Bs-phe_M_signal19.271980
Corner-Avg:11042,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal75.272507
Spike_AFFX-r2-Ec-bioB_3_signal64.579445
Spike_AFFX-r2-Bs-lys_M_signal7.604571
Spike_AFFX-r2-P1-cre_3_signal3060.875244
Spike_AFFX-r2-Bs-lys_3-5-ratio1.413424
Spike_AFFX-r2-Bs-dap_M_signal117.348457
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.453964
Spike_AFFX-r2-Ec-bioB_avg-signal67.389839
Spike_AFFX-r2-Bs-thr_avg-signal38.346535
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal731.625977
Spike_AFFX-r2-Bs-phe_5_signal21.613903
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal981.046326
RawQ2.739800
Spike_AFFX-r2-Bs-lys_5_signal12.140864
Signal(A)2.372200
%A35.032879
Signal(All)139.429382
Corner+Avg:179,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal270.378540
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal17.453323
Spike_AFFX-r2-Ec-bioD_avg-signal856.336182
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.669445
Spike_AFFX-r2-Bs-lys_avg-signal12.301877
Spike_AFFX-r2-P1-cre_avg-signal2895.896484
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.297676
Spike_AFFX-r2-Bs-thr_3_signal62.060661
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-signal19.446402
Spike_AFFX-r2-Bs-dap_3_signal134.477737
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.340912
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal268.668854
#M296
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal17.160194
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.006364
Spike_AFFX-r2-Bs-thr_M_signal35.010998
Signal(P)217.485580
Spike_AFFX-r2-Bs-phe_3-5-ratio0.807504
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8385,Count:9
Spike_AFFX-r2-P1-cre_5_signal2730.917480
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7991
Signal(M)9.746542
BackgroundAvg:67.95,Std:0.58,Min:66.8,Max:69.9
Spike_AFFX-r2-Ec-bioC_avg-signal269.523682
Spike_AFFX-r2-Bs-dap_avg-signal94.616783
Spike_AFFX-r2-Bs-dap_3-5-ratio4.199260
Spike_AFFX-r2-Ec-bioB_5_signal62.317558
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.324104
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-11_HA-RAP2.12_Hypo_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 ("Licausi_588-11_HA-RAP2.12_Hypo_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-11_HA-RAP2.12_Hypo_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::HA::RAP2.12
Stock Code:
Genetic Background: Col-0
Growth Conditions:
ProtocolArabidopsis plants were grown in single pots (6 cm diameter) filled with commercial soil in a growth chamber with a photoperiod of 8h light and 16h darkness, 60% humidity during the day and 75% humidity during the night. Temperature was kept at 20°C during the light period and 16°C during the night.
Plant Spacingone plant/pot
Temperature18 °C average, 20 °C day, 16 °C night
Humidity67.5 % average, 60 % day, 75 % night
Medium
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.20
Genetic Variation: T-DNA knock out mutation in At1g53910
Tissue: whole rosette
in vivo Treatment: Plants treated for 90 min in the dark at hypoxic conditions (1% O2).
Additional Organism Information:
Sample Descriptionhealthy green plants with 3cm diameter rosette.
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:0.412014
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-ratio1.059436
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.105953
Spike_AFFX-r2-Bs-dap_5_signal31.519409
NoiseAvg:3.28,Std:0.76,Min:2.7,Max:7.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.401997
#P14572
Spike_AFFX-r2-Bs-phe_M_signal14.939730
Corner-Avg:9495,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal91.142006
Spike_AFFX-r2-Ec-bioB_3_signal63.726357
Spike_AFFX-r2-Bs-lys_M_signal10.159434
Spike_AFFX-r2-P1-cre_3_signal2999.163574
Spike_AFFX-r2-Bs-lys_3-5-ratio1.493312
Spike_AFFX-r2-Bs-dap_M_signal110.002548
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.937058
Spike_AFFX-r2-Ec-bioB_avg-signal70.829857
Spike_AFFX-r2-Bs-thr_avg-signal37.453968
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal804.604431
Spike_AFFX-r2-Bs-phe_5_signal16.615488
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1015.932190
RawQ2.798755
Spike_AFFX-r2-Bs-lys_5_signal13.666634
Signal(A)2.815314
%A34.712845
Signal(All)141.595352
Corner+Avg:157,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal244.207230
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.985273
Spike_AFFX-r2-Ec-bioD_avg-signal910.268311
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.884262
Spike_AFFX-r2-Bs-lys_avg-signal14.744870
Spike_AFFX-r2-P1-cre_avg-signal2915.034424
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.402893
Spike_AFFX-r2-Bs-thr_3_signal59.921848
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-signal18.180162
Spike_AFFX-r2-Bs-dap_3_signal113.596245
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.262648
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal271.762177
#M320
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal20.408545
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.898606
Spike_AFFX-r2-Bs-thr_M_signal32.038071
Signal(P)219.855515
Spike_AFFX-r2-Bs-phe_3-5-ratio1.383364
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7326,Count:9
Spike_AFFX-r2-P1-cre_5_signal2830.905273
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7918
Signal(M)11.762472
BackgroundAvg:66.83,Std:1.17,Min:60.4,Max:68.5
Spike_AFFX-r2-Ec-bioC_avg-signal257.984711
Spike_AFFX-r2-Bs-dap_avg-signal85.039398
Spike_AFFX-r2-Bs-dap_3-5-ratio3.604009
Spike_AFFX-r2-Ec-bioB_5_signal57.621208
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.412014
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-12_HA-RAP2.12_Hypo_Rep3_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 ("Licausi_588-12_HA-RAP2.12_Hypo_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-12_HA-RAP2.12_Hypo_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::HA::RAP2.12
Stock Code:
Genetic Background: Col-0
Growth Conditions:
ProtocolArabidopsis plants were grown in single pots (6 cm diameter) filled with commercial soil in a growth chamber with a photoperiod of 8h light and 16h darkness, 60% humidity during the day and 75% humidity during the night. Temperature was kept at 20°C during the light period and 16°C during the night.
Plant Spacingone plant/pot
Temperature18 °C average, 20 °C day, 16 °C night
Humidity67.5 % average, 60 % day, 75 % night
Medium
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.20
Genetic Variation: T-DNA knock out mutation in At1g53910
Tissue: whole rosette
in vivo Treatment: Plants treated for 90 min in the dark at hypoxic conditions (1% O2).
Additional Organism Information:
Sample Descriptionhealthy green plants with 3cm diameter rosette.
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:0.401633
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-ratio1.216978
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.102236
Spike_AFFX-r2-Bs-dap_5_signal37.599941
NoiseAvg:3.16,Std:0.07,Min:2.9,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_signal20.899721
#P14525
Spike_AFFX-r2-Bs-phe_M_signal20.626518
Corner-Avg:10296,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal74.298515
Spike_AFFX-r2-Ec-bioB_3_signal65.034180
Spike_AFFX-r2-Bs-lys_M_signal10.556703
Spike_AFFX-r2-P1-cre_3_signal3222.307129
Spike_AFFX-r2-Bs-lys_3-5-ratio1.143484
Spike_AFFX-r2-Bs-dap_M_signal122.015419
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.220482
Spike_AFFX-r2-Ec-bioB_avg-signal66.111588
Spike_AFFX-r2-Bs-thr_avg-signal44.464741
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal655.062500
Spike_AFFX-r2-Bs-phe_5_signal21.097137
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal983.747620
RawQ2.884794
Spike_AFFX-r2-Bs-lys_5_signal15.827926
Signal(A)3.153374
%A34.563789
Signal(All)140.962433
Corner+Avg:166,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal238.580704
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.938637
Spike_AFFX-r2-Ec-bioD_avg-signal819.405029
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.678211
Spike_AFFX-r2-Bs-lys_avg-signal14.827872
Spike_AFFX-r2-P1-cre_avg-signal2935.050293
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.758001
Spike_AFFX-r2-Bs-thr_3_signal67.307182
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-signal21.554098
Spike_AFFX-r2-Bs-dap_3_signal150.367554
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.501761
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal235.694702
#M401
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.098986
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.012245
Spike_AFFX-r2-Bs-thr_M_signal45.187325
Signal(P)219.323532
Spike_AFFX-r2-Bs-phe_3-5-ratio1.087287
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7477,Count:9
Spike_AFFX-r2-P1-cre_5_signal2647.793457
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7884
Signal(M)12.014132
BackgroundAvg:68.69,Std:0.62,Min:67.3,Max:71.0
Spike_AFFX-r2-Ec-bioC_avg-signal237.137695
Spike_AFFX-r2-Bs-dap_avg-signal103.327637
Spike_AFFX-r2-Bs-dap_3-5-ratio3.999143
Spike_AFFX-r2-Ec-bioB_5_signal59.002056
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.401633
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-13_ami-RAP_Control_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 ("Licausi_588-13_ami-RAP_Control_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-13_ami-RAP_Control_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: amiRAP2.2-12
Stock Code:
Genetic Background: Col-0
Growth Conditions:
ProtocolArabidopsis plants were grown in single pots (6 cm diameter) filled with commercial soil in a growth chamber with a photoperiod of 8h light and 16h darkness, 60% humidity during the day and 75% humidity during the night. Temperature was kept at 20°C during the light period and 16°C during the night.
Plant Spacingone plant/pot
Temperature18 °C average, 20 °C day, 16 °C night
Humidity67.5 % average, 60 % day, 75 % night
Medium
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.20
Genetic Variation: T-DNA knock out mutation in At1g53910,At2g14230
Tissue: whole rosette
in vivo Treatment: Plants treated for 90 min in the dark at normoxic conditions (21% O2).
Additional Organism Information:
Sample Descriptionhealthy green plants with 3cm diameter rosette.
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:0.397759
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-ratio0.947080
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.070959
Spike_AFFX-r2-Bs-dap_5_signal51.367466
NoiseAvg:2.80,Std:0.13,Min:2.4,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_signal28.049728
#P14651
Spike_AFFX-r2-Bs-phe_M_signal36.699703
Corner-Avg:10478,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal76.576302
Spike_AFFX-r2-Ec-bioB_3_signal63.622890
Spike_AFFX-r2-Bs-lys_M_signal11.876904
Spike_AFFX-r2-P1-cre_3_signal2502.560547
Spike_AFFX-r2-Bs-lys_3-5-ratio1.485255
Spike_AFFX-r2-Bs-dap_M_signal142.324463
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.937925
Spike_AFFX-r2-Ec-bioB_avg-signal66.535538
Spike_AFFX-r2-Bs-thr_avg-signal65.982857
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal604.594543
Spike_AFFX-r2-Bs-phe_5_signal33.618748
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal965.129822
RawQ2.568026
Spike_AFFX-r2-Bs-lys_5_signal21.218317
Signal(A)2.649027
%A34.274441
Signal(All)143.096939
Corner+Avg:177,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal207.013687
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal31.674227
Spike_AFFX-r2-Ec-bioD_avg-signal784.862183
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.230598
Spike_AFFX-r2-Bs-lys_avg-signal21.536606
Spike_AFFX-r2-P1-cre_avg-signal2572.478027
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.494958
Spike_AFFX-r2-Bs-thr_3_signal110.457718
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-signal33.997559
Spike_AFFX-r2-Bs-dap_3_signal221.411209
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.596326
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal224.550751
#M341
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal31.514601
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.921902
Spike_AFFX-r2-Bs-thr_M_signal59.441128
Signal(P)221.123489
Spike_AFFX-r2-Bs-phe_3-5-ratio0.942160
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7339,Count:9
Spike_AFFX-r2-P1-cre_5_signal2642.395752
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7818
Signal(M)10.706280
BackgroundAvg:62.29,Std:0.73,Min:60.5,Max:64.2
Spike_AFFX-r2-Ec-bioC_avg-signal215.782227
Spike_AFFX-r2-Bs-dap_avg-signal138.367706
Spike_AFFX-r2-Bs-dap_3-5-ratio4.310339
Spike_AFFX-r2-Ec-bioB_5_signal59.407425
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.397759
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-14_ami-RAP_Control_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 ("Licausi_588-14_ami-RAP_Control_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-14_ami-RAP_Control_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: amiRAP2.2-12
Stock Code:
Genetic Background: Col-0
Growth Conditions:
ProtocolArabidopsis plants were grown in single pots (6 cm diameter) filled with commercial soil in a growth chamber with a photoperiod of 8h light and 16h darkness, 60% humidity during the day and 75% humidity during the night. Temperature was kept at 20°C during the light period and 16°C during the night.
Plant Spacingone plant/pot
Temperature18 °C average, 20 °C day, 16 °C night
Humidity67.5 % average, 60 % day, 75 % night
Medium
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.20
Genetic Variation: T-DNA knock out mutation in At1g53910,At2g14230
Tissue: whole rosette
in vivo Treatment: Plants treated for 90 min in the dark at normoxic conditions (21% O2).
Additional Organism Information:
Sample Descriptionhealthy green plants with 3cm diameter rosette.
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:0.419536
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-ratio1.219374
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.114949
Spike_AFFX-r2-Bs-dap_5_signal57.051788
NoiseAvg:2.91,Std:0.11,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_signal40.698448
#P14354
Spike_AFFX-r2-Bs-phe_M_signal38.058914
Corner-Avg:10000,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal83.548462
Spike_AFFX-r2-Ec-bioB_3_signal60.065109
Spike_AFFX-r2-Bs-lys_M_signal10.619255
Spike_AFFX-r2-P1-cre_3_signal3197.476807
Spike_AFFX-r2-Bs-lys_3-5-ratio1.578416
Spike_AFFX-r2-Bs-dap_M_signal198.495056
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.537844
Spike_AFFX-r2-Ec-bioB_avg-signal65.828697
Spike_AFFX-r2-Bs-thr_avg-signal74.303749
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal673.819397
Spike_AFFX-r2-Bs-phe_5_signal37.416557
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1003.292542
RawQ2.613545
Spike_AFFX-r2-Bs-lys_5_signal25.053770
Signal(A)2.924255
%A35.523891
Signal(All)141.621078
Corner+Avg:163,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal251.334824
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal46.541576
Spike_AFFX-r2-Ec-bioD_avg-signal838.555969
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.928539
Spike_AFFX-r2-Bs-lys_avg-signal25.072763
Spike_AFFX-r2-P1-cre_avg-signal2909.852783
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.547567
Spike_AFFX-r2-Bs-thr_3_signal103.286324
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-signal40.672352
Spike_AFFX-r2-Bs-dap_3_signal268.035126
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.488964
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal234.491684
#M353
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal39.545269
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.071828
Spike_AFFX-r2-Bs-thr_M_signal78.926468
Signal(P)223.118317
Spike_AFFX-r2-Bs-phe_3-5-ratio1.243876
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8002,Count:9
Spike_AFFX-r2-P1-cre_5_signal2622.228760
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8103
Signal(M)11.448110
BackgroundAvg:62.84,Std:0.53,Min:61.4,Max:64.0
Spike_AFFX-r2-Ec-bioC_avg-signal242.913254
Spike_AFFX-r2-Bs-dap_avg-signal174.527328
Spike_AFFX-r2-Bs-dap_3-5-ratio4.698102
Spike_AFFX-r2-Ec-bioB_5_signal53.872517
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.419536
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-15_ami-RAP_Control_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 ("Licausi_588-15_ami-RAP_Control_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-15_ami-RAP_Control_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: amiRAP2.2-12
Stock Code:
Genetic Background: Col-0
Growth Conditions:
ProtocolArabidopsis plants were grown in single pots (6 cm diameter) filled with commercial soil in a growth chamber with a photoperiod of 8h light and 16h darkness, 60% humidity during the day and 75% humidity during the night. Temperature was kept at 20°C during the light period and 16°C during the night.
Plant Spacingone plant/pot
Temperature18 °C average, 20 °C day, 16 °C night
Humidity67.5 % average, 60 % day, 75 % night
Medium
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.20
Genetic Variation: T-DNA knock out mutation in At1g53910,At2g14230
Tissue: whole rosette
in vivo Treatment: Plants treated for 90 min in the dark at normoxic conditions (21% O2).
Additional Organism Information:
Sample Descriptionhealthy green plants with 3cm diameter rosette.
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:0.29582
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-ratio1.223964
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.251848
Spike_AFFX-r2-Bs-dap_5_signal35.280064
NoiseAvg:3.27,Std:0.09,Min:3.1,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal22.418116
#P14486
Spike_AFFX-r2-Bs-phe_M_signal36.645302
Corner-Avg:11113,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal60.846539
Spike_AFFX-r2-Ec-bioB_3_signal55.698280
Spike_AFFX-r2-Bs-lys_M_signal13.175754
Spike_AFFX-r2-P1-cre_3_signal3092.883545
Spike_AFFX-r2-Bs-lys_3-5-ratio2.537869
Spike_AFFX-r2-Bs-dap_M_signal172.227646
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.398619
Spike_AFFX-r2-Ec-bioB_avg-signal53.679226
Spike_AFFX-r2-Bs-thr_avg-signal59.740498
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal616.646851
Spike_AFFX-r2-Bs-phe_5_signal38.816074
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal942.434631
RawQ2.966145
Spike_AFFX-r2-Bs-lys_5_signal23.044556
Signal(A)2.424799
%A35.111794
Signal(All)141.227310
Corner+Avg:184,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal206.689331
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal34.288036
Spike_AFFX-r2-Ec-bioD_avg-signal779.540771
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.507233
Spike_AFFX-r2-Bs-lys_avg-signal31.568123
Spike_AFFX-r2-P1-cre_avg-signal2809.911865
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.380973
Spike_AFFX-r2-Bs-thr_3_signal98.608742
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal36.583134
Spike_AFFX-r2-Bs-dap_3_signal226.477188
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.528322
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal231.417267
#M315
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal58.484058
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.893146
Spike_AFFX-r2-Bs-thr_M_signal58.194633
Signal(P)220.815308
Spike_AFFX-r2-Bs-phe_3-5-ratio0.883346
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8701,Count:9
Spike_AFFX-r2-P1-cre_5_signal2526.940186
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8009
Signal(M)10.299002
BackgroundAvg:73.15,Std:0.77,Min:70.6,Max:75.3
Spike_AFFX-r2-Ec-bioC_avg-signal219.053299
Spike_AFFX-r2-Bs-dap_avg-signal144.661636
Spike_AFFX-r2-Bs-dap_3-5-ratio6.419410
Spike_AFFX-r2-Ec-bioB_5_signal44.492855
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.295820
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-16_ami-RAP_Hypo_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 ("Licausi_588-16_ami-RAP_Hypo_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-16_ami-RAP_Hypo_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: amiRAP2.2-12
Stock Code:
Genetic Background: Col-0
Growth Conditions:
ProtocolArabidopsis plants were grown in single pots (6 cm diameter) filled with commercial soil in a growth chamber with a photoperiod of 8h light and 16h darkness, 60% humidity during the day and 75% humidity during the night. Temperature was kept at 20°C during the light period and 16°C during the night.
Plant Spacingone plant/pot
Temperature18 °C average, 20 °C day, 16 °C night
Humidity67.5 % average, 60 % day, 75 % night
Medium
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.20
Genetic Variation: T-DNA knock out mutation in At1g53910,At2g14230
Tissue: whole rosette
in vivo Treatment: Plants treated for 90 min in the dark at normoxic conditions (21% O2).
Additional Organism Information:
Sample Descriptionhealthy green plants with 3cm diameter rosette.
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:0.339801
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-ratio1.174811
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.047436
Spike_AFFX-r2-Bs-dap_5_signal70.395203
NoiseAvg:2.99,Std:0.07,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_signal37.135517
#P14694
Spike_AFFX-r2-Bs-phe_M_signal39.446606
Corner-Avg:11763,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal80.601807
Spike_AFFX-r2-Ec-bioB_3_signal61.620525
Spike_AFFX-r2-Bs-lys_M_signal19.096313
Spike_AFFX-r2-P1-cre_3_signal3099.233398
Spike_AFFX-r2-Bs-lys_3-5-ratio1.337653
Spike_AFFX-r2-Bs-dap_M_signal236.801361
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.178982
Spike_AFFX-r2-Ec-bioB_avg-signal67.017395
Spike_AFFX-r2-Bs-thr_avg-signal78.511856
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal664.618286
Spike_AFFX-r2-Bs-phe_5_signal41.185925
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal939.320923
RawQ2.727804
Spike_AFFX-r2-Bs-lys_5_signal26.136654
Signal(A)2.663221
%A34.042088
Signal(All)140.655380
Corner+Avg:193,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal228.661545
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal35.306511
Spike_AFFX-r2-Ec-bioD_avg-signal801.969604
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.419113
Spike_AFFX-r2-Bs-lys_avg-signal26.731577
Spike_AFFX-r2-P1-cre_avg-signal2868.651855
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.538799
Spike_AFFX-r2-Bs-thr_3_signal118.053146
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-signal38.646347
Spike_AFFX-r2-Bs-dap_3_signal302.097412
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.413324
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal220.635330
#M351
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal34.961761
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.036378
Spike_AFFX-r2-Bs-thr_M_signal80.346916
Signal(P)216.686279
Spike_AFFX-r2-Bs-phe_3-5-ratio0.857247
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9540,Count:9
Spike_AFFX-r2-P1-cre_5_signal2638.070068
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7765
Signal(M)10.487215
BackgroundAvg:65.62,Std:0.65,Min:63.8,Max:67.1
Spike_AFFX-r2-Ec-bioC_avg-signal224.648438
Spike_AFFX-r2-Bs-dap_avg-signal203.098007
Spike_AFFX-r2-Bs-dap_3-5-ratio4.291449
Spike_AFFX-r2-Ec-bioB_5_signal58.829857
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.339801
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-17_ami-RAP_Hypo_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 ("Licausi_588-17_ami-RAP_Hypo_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-17_ami-RAP_Hypo_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: amiRAP2.2-12
Stock Code:
Genetic Background: Col-0
Growth Conditions:
ProtocolArabidopsis plants were grown in single pots (6 cm diameter) filled with commercial soil in a growth chamber with a photoperiod of 8h light and 16h darkness, 60% humidity during the day and 75% humidity during the night. Temperature was kept at 20°C during the light period and 16°C during the night.
Plant Spacingone plant/pot
Temperature18 °C average, 20 °C day, 16 °C night
Humidity67.5 % average, 60 % day, 75 % night
Medium
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.20
Genetic Variation: T-DNA knock out mutation in At1g53910,At2g14230
Tissue: whole rosette
in vivo Treatment: Plants treated for 90 min in the dark at normoxic conditions (21% O2).
Additional Organism Information:
Sample Descriptionhealthy green plants with 3cm diameter rosette.
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:0.611043
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-ratio1.321885
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.024626
Spike_AFFX-r2-Bs-dap_5_signal55.427490
NoiseAvg:2.51,Std:0.09,Min:2.3,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal23.293623
#P13539
Spike_AFFX-r2-Bs-phe_M_signal27.171108
Corner-Avg:9723,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal99.195526
Spike_AFFX-r2-Ec-bioB_3_signal73.758568
Spike_AFFX-r2-Bs-lys_M_signal12.623768
Spike_AFFX-r2-P1-cre_3_signal4732.949707
Spike_AFFX-r2-Bs-lys_3-5-ratio1.349128
Spike_AFFX-r2-Bs-dap_M_signal157.441574
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.094790
Spike_AFFX-r2-Ec-bioB_avg-signal81.646637
Spike_AFFX-r2-Bs-thr_avg-signal73.077888
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal900.322937
Spike_AFFX-r2-Bs-phe_5_signal36.165649
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1153.415649
RawQ2.550308
Spike_AFFX-r2-Bs-lys_5_signal22.931654
Signal(A)3.584252
%A38.838230
Signal(All)147.936401
Corner+Avg:151,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal383.826813
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal41.113029
Spike_AFFX-r2-Ec-bioD_avg-signal1026.869263
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.355545
Spike_AFFX-r2-Bs-lys_avg-signal22.164385
Spike_AFFX-r2-P1-cre_avg-signal4156.702637
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.806225
Spike_AFFX-r2-Bs-thr_3_signal118.676132
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-signal34.816593
Spike_AFFX-r2-Bs-dap_3_signal242.640762
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.281113
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal408.197510
#M412
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal30.937733
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.940297
Spike_AFFX-r2-Bs-thr_M_signal77.263916
Signal(P)246.469925
Spike_AFFX-r2-Bs-phe_3-5-ratio1.136798
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8186,Count:9
Spike_AFFX-r2-P1-cre_5_signal3580.455566
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8859
Signal(M)13.883931
BackgroundAvg:58.41,Std:0.58,Min:56.7,Max:59.7
Spike_AFFX-r2-Ec-bioC_avg-signal396.012146
Spike_AFFX-r2-Bs-dap_avg-signal151.836609
Spike_AFFX-r2-Bs-dap_3-5-ratio4.377625
Spike_AFFX-r2-Ec-bioB_5_signal71.985809
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.611043
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-18_ami-RAP_Hypo_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 ("Licausi_588-18_ami-RAP_Hypo_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-18_ami-RAP_Hypo_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: amiRAP2.2-12
Stock Code:
Genetic Background: Col-0
Growth Conditions:
ProtocolArabidopsis plants were grown in single pots (6 cm diameter) filled with commercial soil in a growth chamber with a photoperiod of 8h light and 16h darkness, 60% humidity during the day and 75% humidity during the night. Temperature was kept at 20°C during the light period and 16°C during the night.
Plant Spacingone plant/pot
Temperature18 °C average, 20 °C day, 16 °C night
Humidity67.5 % average, 60 % day, 75 % night
Medium
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.20
Genetic Variation: T-DNA knock out mutation in At1g53910,At2g14230
Tissue: whole rosette
in vivo Treatment: Plants treated for 90 min in the dark at hypoxic conditions (1% O2).
Additional Organism Information:
Sample Descriptionhealthy green plants with 3cm diameter rosette.
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:0.556504
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-ratio1.213981
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.782844
Spike_AFFX-r2-Bs-dap_5_signal53.182819
NoiseAvg:2.58,Std:0.07,Min:2.4,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal37.050613
#P14099
Spike_AFFX-r2-Bs-phe_M_signal40.859493
Corner-Avg:10367,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal122.706833
Spike_AFFX-r2-Ec-bioB_3_signal72.201004
Spike_AFFX-r2-Bs-lys_M_signal10.560113
Spike_AFFX-r2-P1-cre_3_signal4535.731934
Spike_AFFX-r2-Bs-lys_3-5-ratio1.182863
Spike_AFFX-r2-Bs-dap_M_signal222.574661
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.995979
Spike_AFFX-r2-Ec-bioB_avg-signal95.712318
Spike_AFFX-r2-Bs-thr_avg-signal82.760468
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1022.082214
Spike_AFFX-r2-Bs-phe_5_signal40.001774
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1497.539429
RawQ2.595524
Spike_AFFX-r2-Bs-lys_5_signal27.081308
Signal(A)3.041755
%A36.597984
Signal(All)146.597351
Corner+Avg:164,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal309.578308
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal40.428158
Spike_AFFX-r2-Ec-bioD_avg-signal1259.810791
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.810608
Spike_AFFX-r2-Bs-lys_avg-signal23.224968
Spike_AFFX-r2-P1-cre_avg-signal4135.988770
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.591407
Spike_AFFX-r2-Bs-thr_3_signal148.053467
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-signal40.429810
Spike_AFFX-r2-Bs-dap_3_signal258.714996
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.465185
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal381.282043
#M363
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal32.033485
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.811940
Spike_AFFX-r2-Bs-thr_M_signal63.177322
Signal(P)235.054443
Spike_AFFX-r2-Bs-phe_3-5-ratio1.010659
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7751,Count:9
Spike_AFFX-r2-P1-cre_5_signal3736.245850
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8348
Signal(M)12.288374
BackgroundAvg:58.27,Std:0.34,Min:57.5,Max:59.5
Spike_AFFX-r2-Ec-bioC_avg-signal345.430176
Spike_AFFX-r2-Bs-dap_avg-signal178.157486
Spike_AFFX-r2-Bs-dap_3-5-ratio4.864635
Spike_AFFX-r2-Ec-bioB_5_signal92.229118
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.556504
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-19_35S::HA::ERF16 _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 ("Licausi_588-19_35S::HA::ERF16 _Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-19_35S::HA::ERF16 _Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::HA::ERF16
Stock Code:
Genetic Background: Col-0
Growth Conditions:
ProtocolArabidopsis plants were grown in single pots (6 cm diameter) filled with commercial soil in a growth chamber with a photoperiod of 8h light and 16h darkness, 60% humidity during the day and 75% humidity during the night. Temperature was kept at 20°C during the light period and 16°C during the night.
Plant Spacingone plant/pot
Temperature18 °C average, 20 °C day, 16 °C night
Humidity67.5 % average, 60 % day, 75 % night
Medium
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.20
Genetic Variation: T-DNA knock out mutation in At5g21960
Tissue: whole rosette
Additional Organism Information:
Sample Descriptionhealthy green plants with 3cm diameter rosette.
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:0.312866
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-ratio1.219358
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.917329
Spike_AFFX-r2-Bs-dap_5_signal56.695633
NoiseAvg:2.89,Std:0.06,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_signal35.333714
#P14784
Spike_AFFX-r2-Bs-phe_M_signal39.209202
Corner-Avg:10273,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal76.259178
Spike_AFFX-r2-Ec-bioB_3_signal54.429790
Spike_AFFX-r2-Bs-lys_M_signal12.432467
Spike_AFFX-r2-P1-cre_3_signal2940.576904
Spike_AFFX-r2-Bs-lys_3-5-ratio1.211366
Spike_AFFX-r2-Bs-dap_M_signal229.595016
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.615049
Spike_AFFX-r2-Ec-bioB_avg-signal63.341351
Spike_AFFX-r2-Bs-thr_avg-signal76.453644
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal663.184570
Spike_AFFX-r2-Bs-phe_5_signal43.601471
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal914.923218
RawQ2.613183
Spike_AFFX-r2-Bs-lys_5_signal24.049507
Signal(A)2.304391
%A33.853573
Signal(All)138.964493
Corner+Avg:173,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal211.218719
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal47.225430
Spike_AFFX-r2-Ec-bioD_avg-signal789.053894
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.813675
Spike_AFFX-r2-Bs-lys_avg-signal21.871572
Spike_AFFX-r2-P1-cre_avg-signal2676.077148
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.332749
Spike_AFFX-r2-Bs-thr_3_signal127.733116
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-signal43.345367
Spike_AFFX-r2-Bs-dap_3_signal298.481354
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.379591
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal226.342010
#M304
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal29.132744
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.933184
Spike_AFFX-r2-Bs-thr_M_signal66.294113
Signal(P)213.000687
Spike_AFFX-r2-Bs-phe_3-5-ratio1.083115
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7620,Count:9
Spike_AFFX-r2-P1-cre_5_signal2411.577148
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7722
Signal(M)9.813541
BackgroundAvg:61.12,Std:0.32,Min:60.4,Max:62.2
Spike_AFFX-r2-Ec-bioC_avg-signal218.780365
Spike_AFFX-r2-Bs-dap_avg-signal194.923996
Spike_AFFX-r2-Bs-dap_3-5-ratio5.264627
Spike_AFFX-r2-Ec-bioB_5_signal59.335075
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.312866
NF1.000000
HZ4
Tau0.015000

Slide: Licausi_588-20_35S::HA::ERF16 _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 ("Licausi_588-20_35S::HA::ERF16 _Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Licausi_588-20_35S::HA::ERF16 _Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: 35S::HA::ERF16
Stock Code:
Genetic Background: Col-0
Growth Conditions:
ProtocolArabidopsis plants were grown in single pots (6 cm diameter) filled with commercial soil in a growth chamber with a photoperiod of 8h light and 16h darkness, 60% humidity during the day and 75% humidity during the night. Temperature was kept at 20°C during the light period and 16°C during the night.
Plant Spacingone plant/pot
Temperature18 °C average, 20 °C day, 16 °C night
Humidity67.5 % average, 60 % day, 75 % night
Medium
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.20
Genetic Variation: T-DNA knock out mutation in At5g21960
Tissue: whole rosette
Additional Organism Information:
Sample Descriptionhealthy green plants with 3cm diameter rosette.
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:0.580259
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-ratio1.150228
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.027721
Spike_AFFX-r2-Bs-dap_5_signal52.829025
NoiseAvg:2.57,Std:0.05,Min:2.4,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal30.589216
#P14309
Spike_AFFX-r2-Bs-phe_M_signal24.671076
Corner-Avg:8493,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal81.426842
Spike_AFFX-r2-Ec-bioB_3_signal67.959671
Spike_AFFX-r2-Bs-lys_M_signal20.373632
Spike_AFFX-r2-P1-cre_3_signal3439.850830
Spike_AFFX-r2-Bs-lys_3-5-ratio1.284310
Spike_AFFX-r2-Bs-dap_M_signal166.265228
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.963548
Spike_AFFX-r2-Ec-bioB_avg-signal71.837700
Spike_AFFX-r2-Bs-thr_avg-signal81.247299
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal874.300537
Spike_AFFX-r2-Bs-phe_5_signal34.918320
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1122.730347
RawQ2.562483
Spike_AFFX-r2-Bs-lys_5_signal19.035208
Signal(A)3.340950
%A35.703640
Signal(All)145.470413
Corner+Avg:138,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal254.927902
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal24.097956
Spike_AFFX-r2-Ec-bioD_avg-signal998.515442
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.731258
Spike_AFFX-r2-Bs-lys_avg-signal21.285316
Spike_AFFX-r2-P1-cre_avg-signal3215.216553
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.565103
Spike_AFFX-r2-Bs-thr_3_signal151.831039
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-signal27.895782
Spike_AFFX-r2-Bs-dap_3_signal202.077271
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.284147
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal308.476654
#M357
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.447105
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.826409
Spike_AFFX-r2-Bs-thr_M_signal61.321640
Signal(P)229.664429
Spike_AFFX-r2-Bs-phe_3-5-ratio0.690124
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5915,Count:9
Spike_AFFX-r2-P1-cre_5_signal2990.582275
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8144
Signal(M)13.174108
BackgroundAvg:61.28,Std:0.34,Min:60.5,Max:62.1
Spike_AFFX-r2-Ec-bioC_avg-signal281.702271
Spike_AFFX-r2-Bs-dap_avg-signal140.390503
Spike_AFFX-r2-Bs-dap_3-5-ratio3.825118
Spike_AFFX-r2-Ec-bioB_5_signal66.126587
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.580259
NF1.000000
HZ4
Tau0.015000


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