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Experiment: Direct downstream targets of the transcription factor JAGGED in floral tissue

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-605

The aim of the experiment was to identify direct downstream targets of the transcription factor JAGGED that has been reported to be a key regulator in floral organ outgrowth (Dinneny et al. 2004, Ohno et. al. 2004) downstream of floral organ identity genes such as AGAMOUS (Gomez et al. 2005). For the experiment, plant line 22.11.1.27 that is homozygous for the DEX inducible 35S::JAG:GR construct in Ler background and jag-1 mutant in Ler background were used. Plants were grown on soil under long day conditions with 16 h light, with 20° C day temperature and 18° C night temperature. At flowering, siliques and open flowers were removed from the main inflorescence. Plants were recovered from dissection for 18 h. For induction, main inflorescence was dipped into solutions containing 0.015 % SILWET supplemented with 0.1% EtOH for control treatment of 22.11.3.27 (treatment label E) and jag-1 mutant (treatment label JEG), 10µM Dexamethasone (treatment label DEX), 10 µM Dexamethasone and 10 µM Cycloheximide (treatment label D+C), and Cycloheximide (treatment label C). Plants were incubated for 5 hours for induction. Experiment was performed in 3 replications.

About the Experimenter

Name: Katharina Schiessl
Head of Lab Name:Dr Robert Sablowski
Lab:
Address:Department of Cell and Developmental Biology, John Innes Centre
Norwich Research Park, Colney Lane, Norwich, Norfolk, NR4 7UH, UNITED KINGDOM
Postcode:
Country:
 
Telephone Number: +44 (0)1603 450000
Fax Number: +44 (0)1603 45004

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

About this Experiment

Experiment Type: compound_based_treatment
Number of Slides:15
 
Experimental Parameters:
parametercompound_based_treatment
Quality Control Measures Taken:
References: Dinneny et al. 2004, Ohno et. al. 2004;Gomez et al. 2005.
 
Other Information:

Slides in this Experiment

Hybridisation Set: Schiessl: Direct downstream targets of the transcription factor JAGGED in floral tissue

Slide: Schiessl_605-1_EtOH-Cont_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 ("Schiessl_605-1_EtOH-Cont_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: Schiessl_605-1_EtOH-Cont_Rep1_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.331471
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-ratio1.188105
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.681160
Spike_AFFX-r2-Bs-dap_5_signal58.592648
NoiseAvg:3.91,Std:0.13,Min:3.6,Max:4.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.852455
#P15244
Spike_AFFX-r2-Bs-phe_M_signal55.073853
Corner-Avg:15771,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal18.670944
Spike_AFFX-r2-Ec-bioB_3_signal22.501505
Spike_AFFX-r2-Bs-lys_M_signal57.700691
Spike_AFFX-r2-P1-cre_3_signal3314.539795
Spike_AFFX-r2-Bs-lys_3-5-ratio2.115216
Spike_AFFX-r2-Bs-dap_M_signal374.758759
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio31.720209
Spike_AFFX-r2-Ec-bioB_avg-signal18.185654
Spike_AFFX-r2-Bs-thr_avg-signal112.390656
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal821.828735
Spike_AFFX-r2-Bs-phe_5_signal45.577518
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1087.718140
RawQ3.079731
Spike_AFFX-r2-Bs-lys_5_signal48.201328
Signal(A)3.648267
%A31.547567
Signal(All)136.214371
Corner+Avg:278,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal216.186356
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal131.052216
Spike_AFFX-r2-Ec-bioD_avg-signal954.773438
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.830338
Spike_AFFX-r2-Bs-lys_avg-signal69.286072
Spike_AFFX-r2-P1-cre_avg-signal3052.154297
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_signal280.801727
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-signal77.234528
Spike_AFFX-r2-Bs-dap_3_signal738.481079
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.323534
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal204.039429
#M370
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal101.956207
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.059532
Spike_AFFX-r2-Bs-thr_M_signal47.517807
Signal(P)201.736694
Spike_AFFX-r2-Bs-phe_3-5-ratio2.875370
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12282,Count:9
Spike_AFFX-r2-P1-cre_5_signal2789.769043
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7196
Signal(M)14.925695
BackgroundAvg:73.58,Std:0.87,Min:71.6,Max:75.9
Spike_AFFX-r2-Ec-bioC_avg-signal210.112885
Spike_AFFX-r2-Bs-dap_avg-signal390.610840
Spike_AFFX-r2-Bs-dap_3-5-ratio12.603647
Spike_AFFX-r2-Ec-bioB_5_signal13.384512
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.331471
NF1.000000
HZ4
Tau0.015000

Slide: Schiessl_605-2_EtOH-Cont_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 ("Schiessl_605-2_EtOH-Cont_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: Schiessl_605-2_EtOH-Cont_Rep2_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.387196
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-ratio1.077338
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.711048
Spike_AFFX-r2-Bs-dap_5_signal129.704834
NoiseAvg:3.65,Std:0.22,Min:3.1,Max:4.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal17.404583
#P15728
Spike_AFFX-r2-Bs-phe_M_signal84.800522
Corner-Avg:13836,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal23.522974
Spike_AFFX-r2-Ec-bioB_3_signal16.254278
Spike_AFFX-r2-Bs-lys_M_signal60.656242
Spike_AFFX-r2-P1-cre_3_signal2912.245361
Spike_AFFX-r2-Bs-lys_3-5-ratio1.653718
Spike_AFFX-r2-Bs-dap_M_signal531.020691
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio19.027885
Spike_AFFX-r2-Ec-bioB_avg-signal20.878950
Spike_AFFX-r2-Bs-thr_avg-signal147.607193
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal687.057739
Spike_AFFX-r2-Bs-phe_5_signal123.382790
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1014.090088
RawQ3.026570
Spike_AFFX-r2-Bs-lys_5_signal65.360863
Signal(A)3.600888
%A29.359930
Signal(All)131.897339
Corner+Avg:229,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal225.222351
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal127.775185
Spike_AFFX-r2-Ec-bioD_avg-signal850.573914
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.952217
Spike_AFFX-r2-Bs-lys_avg-signal78.035179
Spike_AFFX-r2-P1-cre_avg-signal2807.715332
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.687856
Spike_AFFX-r2-Bs-thr_3_signal331.172424
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-signal111.986168
Spike_AFFX-r2-Bs-dap_3_signal890.928833
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.475990
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal177.671188
#M385
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal108.088409
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.267636
Spike_AFFX-r2-Bs-thr_M_signal94.244560
Signal(P)189.421707
Spike_AFFX-r2-Bs-phe_3-5-ratio1.035600
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12095,Count:9
Spike_AFFX-r2-P1-cre_5_signal2703.185303
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6697
Signal(M)13.606699
BackgroundAvg:73.02,Std:0.40,Min:71.8,Max:74.4
Spike_AFFX-r2-Ec-bioC_avg-signal201.446777
Spike_AFFX-r2-Bs-dap_avg-signal517.218079
Spike_AFFX-r2-Bs-dap_3-5-ratio6.868895
Spike_AFFX-r2-Ec-bioB_5_signal22.859600
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.387196
NF1.000000
HZ4
Tau0.015000

Slide: Schiessl_605-3_EtOH-Cont_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 ("Schiessl_605-3_EtOH-Cont_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: Schiessl_605-3_EtOH-Cont_Rep3_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.284188
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-ratio1.168622
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.787323
Spike_AFFX-r2-Bs-dap_5_signal33.869057
NoiseAvg:4.49,Std:0.09,Min:4.2,Max:4.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal6.004683
#P15648
Spike_AFFX-r2-Bs-phe_M_signal48.537712
Corner-Avg:14702,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal17.540007
Spike_AFFX-r2-Ec-bioB_3_signal14.869623
Spike_AFFX-r2-Bs-lys_M_signal36.664452
Spike_AFFX-r2-P1-cre_3_signal2810.157471
Spike_AFFX-r2-Bs-lys_3-5-ratio1.819645
Spike_AFFX-r2-Bs-dap_M_signal273.840088
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio31.512531
Spike_AFFX-r2-Ec-bioB_avg-signal17.098648
Spike_AFFX-r2-Bs-thr_avg-signal79.237694
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal671.509949
Spike_AFFX-r2-Bs-phe_5_signal30.425304
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal888.217529
RawQ3.390292
Spike_AFFX-r2-Bs-lys_5_signal38.591705
Signal(A)3.439397
%A29.903551
Signal(All)132.125183
Corner+Avg:249,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal192.262833
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal98.912727
Spike_AFFX-r2-Ec-bioD_avg-signal779.863770
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.601494
Spike_AFFX-r2-Bs-lys_avg-signal48.493122
Spike_AFFX-r2-P1-cre_avg-signal2607.417236
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_signal189.222778
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal59.291916
Spike_AFFX-r2-Bs-dap_3_signal634.023926
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.322717
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal163.702850
#M341
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal70.223221
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.174462
Spike_AFFX-r2-Bs-thr_M_signal42.485619
Signal(P)190.824860
Spike_AFFX-r2-Bs-phe_3-5-ratio3.251002
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12454,Count:9
Spike_AFFX-r2-P1-cre_5_signal2404.677002
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6821
Signal(M)12.574190
BackgroundAvg:89.98,Std:0.94,Min:86.3,Max:92.2
Spike_AFFX-r2-Ec-bioC_avg-signal177.982849
Spike_AFFX-r2-Bs-dap_avg-signal313.911041
Spike_AFFX-r2-Bs-dap_3-5-ratio18.719858
Spike_AFFX-r2-Ec-bioB_5_signal18.886314
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.284188
NF1.000000
HZ4
Tau0.015000

Slide: Schiessl_605-4_dexamethasone_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 ("Schiessl_605-4_dexamethasone_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: Schiessl_605-4_dexamethasone_Rep1_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.437887
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-ratio1.149161
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.933885
Spike_AFFX-r2-Bs-dap_5_signal56.294880
NoiseAvg:4.19,Std:0.19,Min:3.9,Max:5.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.712385
#P15194
Spike_AFFX-r2-Bs-phe_M_signal56.689484
Corner-Avg:13329,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal20.829447
Spike_AFFX-r2-Ec-bioB_3_signal16.848030
Spike_AFFX-r2-Bs-lys_M_signal44.770645
Spike_AFFX-r2-P1-cre_3_signal3422.062744
Spike_AFFX-r2-Bs-lys_3-5-ratio3.431688
Spike_AFFX-r2-Bs-dap_M_signal326.053772
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio22.906544
Spike_AFFX-r2-Ec-bioB_avg-signal18.572760
Spike_AFFX-r2-Bs-thr_avg-signal103.922188
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal901.970764
Spike_AFFX-r2-Bs-phe_5_signal33.349110
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1172.168945
RawQ3.395260
Spike_AFFX-r2-Bs-lys_5_signal26.523878
Signal(A)4.710617
%A31.600176
Signal(All)135.034027
Corner+Avg:238,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal219.702713
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal98.245308
Spike_AFFX-r2-Ec-bioD_avg-signal1037.069824
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.611137
Spike_AFFX-r2-Bs-lys_avg-signal54.105396
Spike_AFFX-r2-P1-cre_avg-signal3199.971436
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.788689
Spike_AFFX-r2-Bs-thr_3_signal245.383713
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-signal62.761295
Spike_AFFX-r2-Bs-dap_3_signal573.199158
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.299564
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal205.968185
#M408
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal91.021667
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.066683
Spike_AFFX-r2-Bs-thr_M_signal55.670471
Signal(P)200.018784
Spike_AFFX-r2-Bs-phe_3-5-ratio2.945965
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10341,Count:9
Spike_AFFX-r2-P1-cre_5_signal2977.880127
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7208
Signal(M)17.369232
BackgroundAvg:85.82,Std:0.96,Min:83.2,Max:88.6
Spike_AFFX-r2-Ec-bioC_avg-signal212.835449
Spike_AFFX-r2-Bs-dap_avg-signal318.515930
Spike_AFFX-r2-Bs-dap_3-5-ratio10.182083
Spike_AFFX-r2-Ec-bioB_5_signal18.040800
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.437887
NF1.000000
HZ4
Tau0.015000

Slide: Schiessl_605-5_dexamethasone_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 ("Schiessl_605-5_dexamethasone_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: Schiessl_605-5_dexamethasone_Rep2_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.418057
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-ratio1.229817
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.190110
Spike_AFFX-r2-Bs-dap_5_signal35.666290
NoiseAvg:4.08,Std:0.20,Min:3.8,Max:4.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.222052
#P15116
Spike_AFFX-r2-Bs-phe_M_signal44.220345
Corner-Avg:14176,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal25.354780
Spike_AFFX-r2-Ec-bioB_3_signal21.827164
Spike_AFFX-r2-Bs-lys_M_signal43.655304
Spike_AFFX-r2-P1-cre_3_signal4121.810547
Spike_AFFX-r2-Bs-lys_3-5-ratio2.252409
Spike_AFFX-r2-Bs-dap_M_signal275.322815
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio26.450220
Spike_AFFX-r2-Ec-bioB_avg-signal21.840805
Spike_AFFX-r2-Bs-thr_avg-signal84.957817
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1131.085693
Spike_AFFX-r2-Bs-phe_5_signal25.526060
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1438.378418
RawQ3.285333
Spike_AFFX-r2-Bs-lys_5_signal30.987513
Signal(A)4.298620
%A32.060501
Signal(All)137.443146
Corner+Avg:234,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal255.914536
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal86.130074
Spike_AFFX-r2-Ec-bioD_avg-signal1284.732056
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.269180
Spike_AFFX-r2-Bs-lys_avg-signal48.146454
Spike_AFFX-r2-P1-cre_avg-signal3736.687256
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.670320
Spike_AFFX-r2-Bs-thr_3_signal191.024857
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-signal51.958828
Spike_AFFX-r2-Bs-dap_3_signal579.307007
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.271679
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal242.839035
#M381
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal69.796547
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.053844
Spike_AFFX-r2-Bs-thr_M_signal56.626545
Signal(P)204.869171
Spike_AFFX-r2-Bs-phe_3-5-ratio3.374202
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11513,Count:9
Spike_AFFX-r2-P1-cre_5_signal3351.563965
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7313
Signal(M)17.951931
BackgroundAvg:86.40,Std:0.87,Min:83.5,Max:88.0
Spike_AFFX-r2-Ec-bioC_avg-signal249.376785
Spike_AFFX-r2-Bs-dap_avg-signal296.765381
Spike_AFFX-r2-Bs-dap_3-5-ratio16.242424
Spike_AFFX-r2-Ec-bioB_5_signal18.340466
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.418057
NF1.000000
HZ4
Tau0.015000

Slide: Schiessl_605-6_dexamethasone_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 ("Schiessl_605-6_dexamethasone_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: Schiessl_605-6_dexamethasone_Rep3_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.310395
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-ratio1.204454
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.429951
Spike_AFFX-r2-Bs-dap_5_signal40.948631
NoiseAvg:4.23,Std:0.23,Min:3.4,Max:4.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal9.244341
#P15628
Spike_AFFX-r2-Bs-phe_M_signal63.557632
Corner-Avg:14844,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal19.012735
Spike_AFFX-r2-Ec-bioB_3_signal17.416819
Spike_AFFX-r2-Bs-lys_M_signal42.132565
Spike_AFFX-r2-P1-cre_3_signal2978.616455
Spike_AFFX-r2-Bs-lys_3-5-ratio2.149022
Spike_AFFX-r2-Bs-dap_M_signal326.342072
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio26.033710
Spike_AFFX-r2-Ec-bioB_avg-signal16.203188
Spike_AFFX-r2-Bs-thr_avg-signal104.044823
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal742.118896
Spike_AFFX-r2-Bs-phe_5_signal50.918591
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1017.642334
RawQ3.361916
Spike_AFFX-r2-Bs-lys_5_signal38.981853
Signal(A)3.601185
%A30.065762
Signal(All)132.569550
Corner+Avg:257,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal220.426132
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal132.109268
Spike_AFFX-r2-Ec-bioD_avg-signal879.880615
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.513809
Spike_AFFX-r2-Bs-lys_avg-signal54.962429
Spike_AFFX-r2-P1-cre_avg-signal2725.809082
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.420430
Spike_AFFX-r2-Bs-thr_3_signal240.664490
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-signal82.195168
Spike_AFFX-r2-Bs-dap_3_signal705.317993
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.371266
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal174.457520
#M324
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal83.772858
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.263495
Spike_AFFX-r2-Bs-thr_M_signal62.225620
Signal(P)191.629150
Spike_AFFX-r2-Bs-phe_3-5-ratio2.594519
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11834,Count:9
Spike_AFFX-r2-P1-cre_5_signal2473.001465
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6858
Signal(M)13.686284
BackgroundAvg:85.91,Std:1.19,Min:82.3,Max:88.2
Spike_AFFX-r2-Ec-bioC_avg-signal197.441833
Spike_AFFX-r2-Bs-dap_avg-signal357.536224
Spike_AFFX-r2-Bs-dap_3-5-ratio17.224459
Spike_AFFX-r2-Ec-bioB_5_signal12.180008
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.310395
NF1.000000
HZ4
Tau0.015000

Slide: Schiessl_605-7_dexamethasone-cycloheximide_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 ("Schiessl_605-7_dexamethasone-cycloheximide_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: Schiessl_605-7_dexamethasone-cycloheximide_Rep1_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.278241
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-ratio1.225621
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.937320
Spike_AFFX-r2-Bs-dap_5_signal40.772339
NoiseAvg:4.68,Std:0.12,Min:4.4,Max:5.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal4.734006
#P16021
Spike_AFFX-r2-Bs-phe_M_signal53.822674
Corner-Avg:15390,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal18.942759
Spike_AFFX-r2-Ec-bioB_3_signal14.832029
Spike_AFFX-r2-Bs-lys_M_signal49.527699
Spike_AFFX-r2-P1-cre_3_signal2861.035645
Spike_AFFX-r2-Bs-lys_3-5-ratio2.394677
Spike_AFFX-r2-Bs-dap_M_signal286.734650
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio42.812794
Spike_AFFX-r2-Ec-bioB_avg-signal16.532887
Spike_AFFX-r2-Bs-thr_avg-signal83.339760
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal717.649658
Spike_AFFX-r2-Bs-phe_5_signal42.677673
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal933.368835
RawQ3.435516
Spike_AFFX-r2-Bs-lys_5_signal33.840981
Signal(A)3.700972
%A28.263920
Signal(All)129.700363
Corner+Avg:280,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal174.926559
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal122.600449
Spike_AFFX-r2-Ec-bioD_avg-signal825.509277
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.236740
Spike_AFFX-r2-Bs-lys_avg-signal54.802296
Spike_AFFX-r2-P1-cre_avg-signal2597.695313
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.499342
Spike_AFFX-r2-Bs-thr_3_signal202.676025
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-signal73.033600
Spike_AFFX-r2-Bs-dap_3_signal647.595093
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.300591
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal157.403061
#M342
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal81.038216
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.111329
Spike_AFFX-r2-Bs-thr_M_signal42.609241
Signal(P)182.856735
Spike_AFFX-r2-Bs-phe_3-5-ratio2.872707
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13588,Count:9
Spike_AFFX-r2-P1-cre_5_signal2334.355225
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6447
Signal(M)14.787889
BackgroundAvg:92.88,Std:1.29,Min:88.6,Max:96.0
Spike_AFFX-r2-Ec-bioC_avg-signal166.164810
Spike_AFFX-r2-Bs-dap_avg-signal325.034027
Spike_AFFX-r2-Bs-dap_3-5-ratio15.883197
Spike_AFFX-r2-Ec-bioB_5_signal15.823873
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.278241
NF1.000000
HZ4
Tau0.015000

Slide: Schiessl_605-8_dexamethasone-cycloheximide_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 ("Schiessl_605-8_dexamethasone-cycloheximide_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: Schiessl_605-8_dexamethasone-cycloheximide_Rep2_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.341263
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-ratio1.180982
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.163020
Spike_AFFX-r2-Bs-dap_5_signal45.915321
NoiseAvg:4.49,Std:0.16,Min:4.0,Max:4.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal6.898030
#P15901
Spike_AFFX-r2-Bs-phe_M_signal49.090946
Corner-Avg:14068,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal18.207756
Spike_AFFX-r2-Ec-bioB_3_signal18.475489
Spike_AFFX-r2-Bs-lys_M_signal38.427238
Spike_AFFX-r2-P1-cre_3_signal3208.318848
Spike_AFFX-r2-Bs-lys_3-5-ratio2.452068
Spike_AFFX-r2-Bs-dap_M_signal290.502167
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio28.570398
Spike_AFFX-r2-Ec-bioB_avg-signal17.523010
Spike_AFFX-r2-Bs-thr_avg-signal84.903549
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal890.128784
Spike_AFFX-r2-Bs-phe_5_signal24.208775
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1048.590454
RawQ3.258218
Spike_AFFX-r2-Bs-lys_5_signal29.994032
Signal(A)3.953576
%A28.658484
Signal(All)130.848511
Corner+Avg:242,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal205.179398
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal91.335274
Spike_AFFX-r2-Ec-bioD_avg-signal969.359619
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.710655
Spike_AFFX-r2-Bs-lys_avg-signal47.322895
Spike_AFFX-r2-P1-cre_avg-signal2962.486816
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.630864
Spike_AFFX-r2-Bs-thr_3_signal197.079468
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-signal54.878330
Spike_AFFX-r2-Bs-dap_3_signal571.440491
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.178021
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal187.020050
#M372
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal73.547417
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.097098
Spike_AFFX-r2-Bs-thr_M_signal50.733162
Signal(P)185.736618
Spike_AFFX-r2-Bs-phe_3-5-ratio3.772817
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12046,Count:9
Spike_AFFX-r2-P1-cre_5_signal2716.654541
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6537
Signal(M)14.548776
BackgroundAvg:85.78,Std:0.70,Min:83.8,Max:87.8
Spike_AFFX-r2-Ec-bioC_avg-signal196.099731
Spike_AFFX-r2-Bs-dap_avg-signal302.619324
Spike_AFFX-r2-Bs-dap_3-5-ratio12.445530
Spike_AFFX-r2-Ec-bioB_5_signal15.885788
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.341263
NF1.000000
HZ4
Tau0.015000

Slide: Schiessl_605-9_dexamethasone-cycloheximide_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 ("Schiessl_605-9_dexamethasone-cycloheximide_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: Schiessl_605-9_dexamethasone-cycloheximide_Rep3_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.371857
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-ratio1.172012
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.464981
Spike_AFFX-r2-Bs-dap_5_signal26.859514
NoiseAvg:4.02,Std:0.13,Min:3.8,Max:4.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal6.387026
#P15981
Spike_AFFX-r2-Bs-phe_M_signal45.125729
Corner-Avg:13745,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal20.075275
Spike_AFFX-r2-Ec-bioB_3_signal22.242905
Spike_AFFX-r2-Bs-lys_M_signal38.444233
Spike_AFFX-r2-P1-cre_3_signal3323.230469
Spike_AFFX-r2-Bs-lys_3-5-ratio2.035710
Spike_AFFX-r2-Bs-dap_M_signal232.618774
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio25.781893
Spike_AFFX-r2-Ec-bioB_avg-signal19.167082
Spike_AFFX-r2-Bs-thr_avg-signal75.041191
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal822.137451
Spike_AFFX-r2-Bs-phe_5_signal37.901226
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal988.492859
RawQ3.164501
Spike_AFFX-r2-Bs-lys_5_signal25.591393
Signal(A)3.947869
%A28.399824
Signal(All)131.420547
Corner+Avg:232,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal207.083328
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal82.731628
Spike_AFFX-r2-Ec-bioD_avg-signal905.315186
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.061378
Spike_AFFX-r2-Bs-lys_avg-signal38.710762
Spike_AFFX-r2-P1-cre_avg-signal3079.361816
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_signal164.669617
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-signal55.252865
Spike_AFFX-r2-Bs-dap_3_signal603.660767
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.202345
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal199.942169
#M351
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal52.096657
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.035716
Spike_AFFX-r2-Bs-thr_M_signal54.066925
Signal(P)185.635818
Spike_AFFX-r2-Bs-phe_3-5-ratio2.182822
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11380,Count:9
Spike_AFFX-r2-P1-cre_5_signal2835.492920
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6478
Signal(M)15.619040
BackgroundAvg:78.21,Std:1.20,Min:76.3,Max:80.8
Spike_AFFX-r2-Ec-bioC_avg-signal203.512756
Spike_AFFX-r2-Bs-dap_avg-signal287.713013
Spike_AFFX-r2-Bs-dap_3-5-ratio22.474747
Spike_AFFX-r2-Ec-bioB_5_signal15.183067
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.371857
NF1.000000
HZ4
Tau0.015000

Slide: Schiessl_605-10_cylcoheximide_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 ("Schiessl_605-10_cylcoheximide_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: Schiessl_605-10_cylcoheximide_Rep1_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.316227
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-ratio1.260571
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.898402
Spike_AFFX-r2-Bs-dap_5_signal24.247169
NoiseAvg:4.09,Std:0.11,Min:3.9,Max:4.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal6.990687
#P16280
Spike_AFFX-r2-Bs-phe_M_signal43.787769
Corner-Avg:13568,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal14.392329
Spike_AFFX-r2-Ec-bioB_3_signal14.086114
Spike_AFFX-r2-Bs-lys_M_signal26.029593
Spike_AFFX-r2-P1-cre_3_signal3065.604736
Spike_AFFX-r2-Bs-lys_3-5-ratio1.589539
Spike_AFFX-r2-Bs-dap_M_signal216.503357
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio24.011417
Spike_AFFX-r2-Ec-bioB_avg-signal14.719176
Spike_AFFX-r2-Bs-thr_avg-signal72.510612
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal735.248962
Spike_AFFX-r2-Bs-phe_5_signal27.055817
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal892.517639
RawQ3.148262
Spike_AFFX-r2-Bs-lys_5_signal27.927958
Signal(A)3.456282
%A27.172293
Signal(All)129.590576
Corner+Avg:226,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal182.548340
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal84.135956
Spike_AFFX-r2-Ec-bioD_avg-signal813.883301
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P71.372208
Spike_AFFX-r2-Bs-lys_avg-signal32.783375
Spike_AFFX-r2-P1-cre_avg-signal2748.761719
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.455502
Spike_AFFX-r2-Bs-thr_3_signal167.856308
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-signal51.659847
Spike_AFFX-r2-Bs-dap_3_signal543.244141
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.213899
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal156.480789
#M332
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal44.392570
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.166586
Spike_AFFX-r2-Bs-thr_M_signal42.684841
Signal(P)179.981339
Spike_AFFX-r2-Bs-phe_3-5-ratio3.109718
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12005,Count:9
Spike_AFFX-r2-P1-cre_5_signal2431.918457
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6198
Signal(M)13.382297
BackgroundAvg:82.31,Std:0.39,Min:81.3,Max:83.2
Spike_AFFX-r2-Ec-bioC_avg-signal169.514557
Spike_AFFX-r2-Bs-dap_avg-signal261.331573
Spike_AFFX-r2-Bs-dap_3-5-ratio22.404436
Spike_AFFX-r2-Ec-bioB_5_signal15.679085
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.316227
NF1.000000
HZ4
Tau0.015000

Slide: Schiessl_605-11_cylcoheximide_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 ("Schiessl_605-11_cylcoheximide_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: Schiessl_605-11_cylcoheximide_Rep2_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.408135
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-ratio1.178263
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.468645
Spike_AFFX-r2-Bs-dap_5_signal27.940678
NoiseAvg:4.06,Std:0.13,Min:3.9,Max:4.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.625143
#P15676
Spike_AFFX-r2-Bs-phe_M_signal45.737316
Corner-Avg:12765,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal16.193148
Spike_AFFX-r2-Ec-bioB_3_signal19.412256
Spike_AFFX-r2-Bs-lys_M_signal35.980354
Spike_AFFX-r2-P1-cre_3_signal3163.471924
Spike_AFFX-r2-Bs-lys_3-5-ratio2.274254
Spike_AFFX-r2-Bs-dap_M_signal241.487946
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio27.229847
Spike_AFFX-r2-Ec-bioB_avg-signal16.274401
Spike_AFFX-r2-Bs-thr_avg-signal85.359352
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal765.165771
Spike_AFFX-r2-Bs-phe_5_signal29.601152
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1027.654053
RawQ3.276638
Spike_AFFX-r2-Bs-lys_5_signal29.159485
Signal(A)4.205888
%A29.697500
Signal(All)132.547699
Corner+Avg:217,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal188.483551
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal76.645187
Spike_AFFX-r2-Ec-bioD_avg-signal896.409912
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.724243
Spike_AFFX-r2-Bs-lys_avg-signal43.818634
Spike_AFFX-r2-P1-cre_avg-signal2924.166016
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.578255
Spike_AFFX-r2-Bs-thr_3_signal207.631470
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-signal50.661221
Spike_AFFX-r2-Bs-dap_3_signal530.062561
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.343048
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal163.951019
#M360
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal66.316071
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.149633
Spike_AFFX-r2-Bs-thr_M_signal40.821461
Signal(P)190.678329
Spike_AFFX-r2-Bs-phe_3-5-ratio2.589264
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9852,Count:9
Spike_AFFX-r2-P1-cre_5_signal2684.860107
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6774
Signal(M)16.247017
BackgroundAvg:86.75,Std:0.75,Min:84.7,Max:89.3
Spike_AFFX-r2-Ec-bioC_avg-signal176.217285
Spike_AFFX-r2-Bs-dap_avg-signal266.497070
Spike_AFFX-r2-Bs-dap_3-5-ratio18.970999
Spike_AFFX-r2-Ec-bioB_5_signal13.217800
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.408135
NF1.000000
HZ4
Tau0.015000

Slide: Schiessl_605-12_cylcoheximide_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 ("Schiessl_605-12_cylcoheximide_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: Schiessl_605-12_cylcoheximide_Rep3_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.357008
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-ratio1.205468
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.882508
Spike_AFFX-r2-Bs-dap_5_signal27.038214
NoiseAvg:4.12,Std:0.16,Min:3.8,Max:4.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.237597
#P16026
Spike_AFFX-r2-Bs-phe_M_signal42.319881
Corner-Avg:13163,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal15.716913
Spike_AFFX-r2-Ec-bioB_3_signal16.219734
Spike_AFFX-r2-Bs-lys_M_signal38.818714
Spike_AFFX-r2-P1-cre_3_signal3029.866943
Spike_AFFX-r2-Bs-lys_3-5-ratio1.718389
Spike_AFFX-r2-Bs-dap_M_signal242.448669
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio21.728819
Spike_AFFX-r2-Ec-bioB_avg-signal16.771927
Spike_AFFX-r2-Bs-thr_avg-signal67.887581
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal693.516418
Spike_AFFX-r2-Bs-phe_5_signal29.764528
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal905.315613
RawQ3.273479
Spike_AFFX-r2-Bs-lys_5_signal31.571997
Signal(A)3.801963
%A28.088558
Signal(All)130.854752
Corner+Avg:209,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal194.302597
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal72.091827
Spike_AFFX-r2-Ec-bioD_avg-signal799.416016
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.258659
Spike_AFFX-r2-Bs-lys_avg-signal41.547901
Spike_AFFX-r2-P1-cre_avg-signal2771.651855
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.652784
Spike_AFFX-r2-Bs-thr_3_signal157.264435
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal48.058746
Spike_AFFX-r2-Bs-dap_3_signal583.820313
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.305399
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal179.461517
#M377
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal54.252983
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.082698
Spike_AFFX-r2-Bs-thr_M_signal39.160725
Signal(P)184.304276
Spike_AFFX-r2-Bs-phe_3-5-ratio2.422072
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12068,Count:9
Spike_AFFX-r2-P1-cre_5_signal2513.436523
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6407
Signal(M)17.977407
BackgroundAvg:86.51,Std:0.72,Min:83.5,Max:88.3
Spike_AFFX-r2-Ec-bioC_avg-signal186.882050
Spike_AFFX-r2-Bs-dap_avg-signal284.435730
Spike_AFFX-r2-Bs-dap_3-5-ratio21.592415
Spike_AFFX-r2-Ec-bioB_5_signal18.379135
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.357008
NF1.000000
HZ4
Tau0.015000

Slide: Schiessl_605-13_EtOH_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 ("Schiessl_605-13_EtOH_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: Schiessl_605-13_EtOH_Rep1_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.420143
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-ratio0.994838
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.126342
Spike_AFFX-r2-Bs-dap_5_signal26.822620
NoiseAvg:3.36,Std:0.09,Min:3.2,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.431374
#P15276
Spike_AFFX-r2-Bs-phe_M_signal45.674648
Corner-Avg:9042,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal50.968666
Spike_AFFX-r2-Ec-bioB_3_signal32.551556
Spike_AFFX-r2-Bs-lys_M_signal32.385681
Spike_AFFX-r2-P1-cre_3_signal2280.522705
Spike_AFFX-r2-Bs-lys_3-5-ratio2.237953
Spike_AFFX-r2-Bs-dap_M_signal315.354797
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio38.851048
Spike_AFFX-r2-Ec-bioB_avg-signal37.473492
Spike_AFFX-r2-Bs-thr_avg-signal128.912720
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal446.547516
Spike_AFFX-r2-Bs-phe_5_signal24.076036
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal561.520264
RawQ2.742293
Spike_AFFX-r2-Bs-lys_5_signal36.272964
Signal(A)4.082103
%A31.420429
Signal(All)134.677307
Corner+Avg:179,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal132.316742
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal103.920219
Spike_AFFX-r2-Ec-bioD_avg-signal504.033875
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.970627
Spike_AFFX-r2-Bs-lys_avg-signal49.945282
Spike_AFFX-r2-P1-cre_avg-signal2286.438965
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.608943
Spike_AFFX-r2-Bs-thr_3_signal327.567688
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal57.890301
Spike_AFFX-r2-Bs-dap_3_signal633.660828
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.257470
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal114.651207
#M367
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal81.177200
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.154081
Spike_AFFX-r2-Bs-thr_M_signal50.739117
Signal(P)198.834412
Spike_AFFX-r2-Bs-phe_3-5-ratio4.316334
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5939,Count:9
Spike_AFFX-r2-P1-cre_5_signal2292.355469
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7167
Signal(M)14.546598
BackgroundAvg:65.76,Std:0.60,Min:63.7,Max:67.0
Spike_AFFX-r2-Ec-bioC_avg-signal123.483978
Spike_AFFX-r2-Bs-dap_avg-signal325.279419
Spike_AFFX-r2-Bs-dap_3-5-ratio23.624121
Spike_AFFX-r2-Ec-bioB_5_signal28.900249
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.420143
NF1.000000
HZ4
Tau0.015000

Slide: Schiessl_605-14_EtOH_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 ("Schiessl_605-14_EtOH_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: Schiessl_605-14_EtOH_Rep2_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.399512
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-ratio1.219246
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.913940
Spike_AFFX-r2-Bs-dap_5_signal24.256531
NoiseAvg:3.30,Std:0.17,Min:2.9,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal2.214085
#P15469
Spike_AFFX-r2-Bs-phe_M_signal49.137321
Corner-Avg:8363,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal46.297756
Spike_AFFX-r2-Ec-bioB_3_signal36.361027
Spike_AFFX-r2-Bs-lys_M_signal48.853428
Spike_AFFX-r2-P1-cre_3_signal2134.186768
Spike_AFFX-r2-Bs-lys_3-5-ratio2.554765
Spike_AFFX-r2-Bs-dap_M_signal227.154541
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio127.229851
Spike_AFFX-r2-Ec-bioB_avg-signal40.814564
Spike_AFFX-r2-Bs-thr_avg-signal111.399658
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal327.427032
Spike_AFFX-r2-Bs-phe_5_signal44.351913
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal683.877625
RawQ2.747226
Spike_AFFX-r2-Bs-lys_5_signal42.133724
Signal(A)3.397488
%A30.534853
Signal(All)134.414902
Corner+Avg:166,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal114.143730
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal95.637878
Spike_AFFX-r2-Ec-bioD_avg-signal505.652344
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.816750
Spike_AFFX-r2-Bs-lys_avg-signal66.209633
Spike_AFFX-r2-P1-cre_avg-signal1942.301270
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.648400
Spike_AFFX-r2-Bs-thr_3_signal281.697693
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-signal63.042374
Spike_AFFX-r2-Bs-dap_3_signal674.191284
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.088641
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal122.787270
#M376
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal107.641754
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.929606
Spike_AFFX-r2-Bs-thr_M_signal50.287212
Signal(P)196.370697
Spike_AFFX-r2-Bs-phe_3-5-ratio2.156342
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5843,Count:9
Spike_AFFX-r2-P1-cre_5_signal1750.415771
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6965
Signal(M)12.452518
BackgroundAvg:67.23,Std:0.64,Min:65.5,Max:69.2
Spike_AFFX-r2-Ec-bioC_avg-signal118.465500
Spike_AFFX-r2-Bs-dap_avg-signal308.534119
Spike_AFFX-r2-Bs-dap_3-5-ratio27.794218
Spike_AFFX-r2-Ec-bioB_5_signal39.784908
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.399512
NF1.000000
HZ4
Tau0.015000

Slide: Schiessl_605-15_EtOH_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 ("Schiessl_605-15_EtOH_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: Schiessl_605-15_EtOH_Rep3_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.479175
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-ratio1.191913
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.026297
Spike_AFFX-r2-Bs-dap_5_signal19.985411
NoiseAvg:2.84,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_signal4.491220
#P15289
Spike_AFFX-r2-Bs-phe_M_signal43.624714
Corner-Avg:7168,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal67.179688
Spike_AFFX-r2-Ec-bioB_3_signal40.471195
Spike_AFFX-r2-Bs-lys_M_signal34.001545
Spike_AFFX-r2-P1-cre_3_signal2799.760498
Spike_AFFX-r2-Bs-lys_3-5-ratio2.222433
Spike_AFFX-r2-Bs-dap_M_signal299.187012
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio71.654373
Spike_AFFX-r2-Ec-bioB_avg-signal49.028362
Spike_AFFX-r2-Bs-thr_avg-signal128.127670
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal522.364258
Spike_AFFX-r2-Bs-phe_5_signal35.988102
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal710.866699
RawQ2.415115
Spike_AFFX-r2-Bs-lys_5_signal36.403660
Signal(A)3.680163
%A31.328365
Signal(All)135.071060
Corner+Avg:124,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal163.393417
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal115.910469
Spike_AFFX-r2-Ec-bioD_avg-signal616.615479
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.027618
Spike_AFFX-r2-Bs-lys_avg-signal50.436634
Spike_AFFX-r2-P1-cre_avg-signal2574.362305
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_signal321.815552
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-signal65.174431
Spike_AFFX-r2-Bs-dap_3_signal681.842896
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.360864
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal155.707504
#M375
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal80.904701
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.049361
Spike_AFFX-r2-Bs-thr_M_signal58.076248
Signal(P)199.448898
Spike_AFFX-r2-Bs-phe_3-5-ratio3.220800
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5441,Count:9
Spike_AFFX-r2-P1-cre_5_signal2348.964111
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7146
Signal(M)14.128807
BackgroundAvg:57.75,Std:0.56,Min:56.4,Max:59.5
Spike_AFFX-r2-Ec-bioC_avg-signal159.550461
Spike_AFFX-r2-Bs-dap_avg-signal333.671783
Spike_AFFX-r2-Bs-dap_3-5-ratio34.117031
Spike_AFFX-r2-Ec-bioB_5_signal39.434204
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.479175
NF1.000000
HZ4
Tau0.015000


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