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Experiment: Sugar responses in Col and pft1-2

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-593

aims: compare gene expression in response to sugar treatment between Col and the pft1-2 mutant. mutant: pft1-2 (Salk_129555), tissues: seedlings, treatment: 3% Glucose for 6 hours, reference for the protocol: ISSN 1088-9051/06, experimental set up: seedlings were grown in vitro for 7 days on MS medium complemented with 0.5% Glucose. After 7 days, the seedlings were transfered in liquid culture in MS without glucose. After 24 hours, the medium was replaced by MS complemented with 3% Glucose for 6 hours.

About the Experimenter

Name:Dr Mathilde SEGUELA
Head of Lab Name: Mike Bevan
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: 01603450516

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, genetic_modification_design
Number of Slides:12
 
Experimental Parameters:
parameter compound_based_treatment
Quality Control Measures Taken:
References: ISSN 1088-9051/06
 
Other Information:

Slides in this Experiment

Hybridisation Set: SEGUELA: sugar responses in Col and pft1-2

Slide: SEGUELA_593-1_Col_0h_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 ("SEGUELA_593-1_Col_0h_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: SEGUELA_593-1_Col_0h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
ProtocolCol-0 seedlings were grown on MS complemented with 0.5% Glucose for 7 days under continous light. After 7 days, seedlings were transfred in liquid culture in a Glucose free MS medium. After 24h, the medium was replaced by MS medium complemented with 3% Glucose. Seedlings were sampled after 6 hours of treatment.
Percentage Agrose10
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
LightingConstant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
in vivo Treatment: 3% Glucose
Additional Organism Information:
Sample Description
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:0.29064
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-ratio1.277028
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.989524
Spike_AFFX-r2-Bs-dap_5_signal50.011158
NoiseAvg:3.60,Std:0.09,Min:3.4,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal23.510202
#P15254
Spike_AFFX-r2-Bs-phe_M_signal16.576237
Corner-Avg:10866,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal54.385632
Spike_AFFX-r2-Ec-bioB_3_signal41.682610
Spike_AFFX-r2-Bs-lys_M_signal11.040221
Spike_AFFX-r2-P1-cre_3_signal2573.182617
Spike_AFFX-r2-Bs-lys_3-5-ratio2.195993
Spike_AFFX-r2-Bs-dap_M_signal153.097580
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.686914
Spike_AFFX-r2-Ec-bioB_avg-signal46.064041
Spike_AFFX-r2-Bs-thr_avg-signal51.502056
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal437.161469
Spike_AFFX-r2-Bs-phe_5_signal17.194399
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal653.024963
RawQ3.056124
Spike_AFFX-r2-Bs-lys_5_signal16.275251
Signal(A)3.187668
%A31.617712
Signal(All)136.651642
Corner+Avg:200,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal170.142532
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal26.132668
Spike_AFFX-r2-Ec-bioD_avg-signal545.093201
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.874176
Spike_AFFX-r2-Bs-lys_avg-signal21.018606
Spike_AFFX-r2-P1-cre_avg-signal2294.079590
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.508111
Spike_AFFX-r2-Bs-thr_3_signal86.680099
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal19.967768
Spike_AFFX-r2-Bs-dap_3_signal219.453751
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.493784
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal150.714462
#M344
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal35.740345
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.128906
Spike_AFFX-r2-Bs-thr_M_signal44.315857
Signal(P)202.531662
Spike_AFFX-r2-Bs-phe_3-5-ratio1.519836
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8272,Count:9
Spike_AFFX-r2-P1-cre_5_signal2014.976685
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7212
Signal(M)13.420470
BackgroundAvg:73.35,Std:0.46,Min:72.1,Max:74.6
Spike_AFFX-r2-Ec-bioC_avg-signal160.428497
Spike_AFFX-r2-Bs-dap_avg-signal140.854172
Spike_AFFX-r2-Bs-dap_3-5-ratio4.388096
Spike_AFFX-r2-Ec-bioB_5_signal42.123886
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.290640
NF1.000000
HZ4
Tau0.015000

Slide: SEGUELA_593-2_Col_0h_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 ("SEGUELA_593-2_Col_0h_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: SEGUELA_593-2_Col_0h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
ProtocolCol-0 seedlings were grown on MS complemented with 0.5% Glucose for 7 days under continous light. After 7 days, seedlings were transfred in liquid culture in a Glucose free MS medium. After 24h, the medium was replaced by MS medium complemented with 3% Glucose. Seedlings were sampled after 6 hours of treatment.
Percentage Agrose10
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
LightingConstant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
in vivo Treatment: 3% Glucose
Additional Organism Information:
Sample Description
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:0.35312
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-ratio1.174914
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.849353
Spike_AFFX-r2-Bs-dap_5_signal62.195980
NoiseAvg:3.42,Std:0.07,Min:3.2,Max:3.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal21.964737
#P15178
Spike_AFFX-r2-Bs-phe_M_signal30.212557
Corner-Avg:10552,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal63.638027
Spike_AFFX-r2-Ec-bioB_3_signal44.711075
Spike_AFFX-r2-Bs-lys_M_signal18.337872
Spike_AFFX-r2-P1-cre_3_signal2817.474365
Spike_AFFX-r2-Bs-lys_3-5-ratio2.348872
Spike_AFFX-r2-Bs-dap_M_signal177.930603
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.532780
Spike_AFFX-r2-Ec-bioB_avg-signal53.663479
Spike_AFFX-r2-Bs-thr_avg-signal71.094429
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal491.436890
Spike_AFFX-r2-Bs-phe_5_signal29.358421
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal757.729004
RawQ3.035056
Spike_AFFX-r2-Bs-lys_5_signal22.602724
Signal(A)3.126124
%A31.898291
Signal(All)139.607758
Corner+Avg:192,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal190.366699
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal29.511669
Spike_AFFX-r2-Ec-bioD_avg-signal624.582947
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.540993
Spike_AFFX-r2-Bs-lys_avg-signal31.343832
Spike_AFFX-r2-P1-cre_avg-signal2607.750000
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.560719
Spike_AFFX-r2-Bs-thr_3_signal121.526062
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal29.694216
Spike_AFFX-r2-Bs-dap_3_signal259.163727
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.541864
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal196.079391
#M356
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal53.090900
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.970865
Spike_AFFX-r2-Bs-thr_M_signal69.792480
Signal(P)208.031219
Spike_AFFX-r2-Bs-phe_3-5-ratio1.005220
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7720,Count:9
Spike_AFFX-r2-P1-cre_5_signal2398.025391
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7276
Signal(M)11.824444
BackgroundAvg:71.19,Std:0.51,Min:70.0,Max:72.4
Spike_AFFX-r2-Ec-bioC_avg-signal193.223053
Spike_AFFX-r2-Bs-dap_avg-signal166.430099
Spike_AFFX-r2-Bs-dap_3-5-ratio4.166889
Spike_AFFX-r2-Ec-bioB_5_signal52.641331
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.353120
NF1.000000
HZ4
Tau0.015000

Slide: SEGUELA_593-3_Col_0h_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 ("SEGUELA_593-3_Col_0h_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: SEGUELA_593-3_Col_0h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
ProtocolCol-0 seedlings were grown on MS complemented with 0.5% Glucose for 7 days under continous light. After 7 days, seedlings were transfred in liquid culture in a Glucose free MS medium. After 24h, the medium was replaced by MS medium complemented with 3% Glucose. Seedlings were sampled after 6 hours of treatment.
Percentage Agrose10
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
LightingConstant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
in vivo Treatment: 3% Glucose
Additional Organism Information:
Sample Description
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:0.384621
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-ratio1.362547
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.687266
Spike_AFFX-r2-Bs-dap_5_signal19.948086
NoiseAvg:3.06,Std:0.11,Min:2.7,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.003436
#P15252
Spike_AFFX-r2-Bs-phe_M_signal10.215194
Corner-Avg:10639,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal62.914207
Spike_AFFX-r2-Ec-bioB_3_signal37.464878
Spike_AFFX-r2-Bs-lys_M_signal3.921354
Spike_AFFX-r2-P1-cre_3_signal3110.373535
Spike_AFFX-r2-Bs-lys_3-5-ratio2.776175
Spike_AFFX-r2-Bs-dap_M_signal77.216469
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.904183
Spike_AFFX-r2-Ec-bioB_avg-signal51.630657
Spike_AFFX-r2-Bs-thr_avg-signal24.482378
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal390.417664
Spike_AFFX-r2-Bs-phe_5_signal10.960549
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal585.091125
RawQ2.726831
Spike_AFFX-r2-Bs-lys_5_signal4.841175
Signal(A)3.001175
%A31.508110
Signal(All)138.968079
Corner+Avg:185,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal197.558228
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal18.220844
Spike_AFFX-r2-Ec-bioD_avg-signal487.754395
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.865410
Spike_AFFX-r2-Bs-lys_avg-signal7.400826
Spike_AFFX-r2-P1-cre_avg-signal2696.568848
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.626480
Spike_AFFX-r2-Bs-thr_3_signal34.860172
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-signal13.132195
Spike_AFFX-r2-Bs-dap_3_signal87.705093
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.498629
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal171.674927
#M371
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal13.439949
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.150769
Spike_AFFX-r2-Bs-thr_M_signal26.583530
Signal(P)206.124252
Spike_AFFX-r2-Bs-phe_3-5-ratio1.662403
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8313,Count:9
Spike_AFFX-r2-P1-cre_5_signal2282.763916
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7187
Signal(M)12.089813
BackgroundAvg:67.46,Std:0.78,Min:65.7,Max:69.8
Spike_AFFX-r2-Ec-bioC_avg-signal184.616577
Spike_AFFX-r2-Bs-dap_avg-signal61.623219
Spike_AFFX-r2-Bs-dap_3-5-ratio4.396667
Spike_AFFX-r2-Ec-bioB_5_signal54.512886
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.384621
NF1.000000
HZ4
Tau0.015000

Slide: SEGUELA_593-4_pft1_0h_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 ("SEGUELA_593-4_pft1_0h_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: SEGUELA_593-4_pft1_0h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_129555 (BZ)
Stock Code: N629555
Genetic Background: Col-0 (Columbia, N60000)
Growth Conditions:
ProtocolCol-0 seedlings were grown on MS complemented with 0.5% Glucose for 7 days under continous light. After 7 days, seedlings were transfred in liquid culture in a Glucose free MS medium. After 24h, the medium was replaced by MS medium complemented with 3% Glucose. Seedlings were sampled after 6 hours of treatment.
Percentage Agrose10
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
LightingConstant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA Insertion
Tissue: whole plant
in vivo Treatment: 3% Glucose
Additional Organism Information:
Sample Description
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:0.448271
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-ratio1.206969
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.065826
Spike_AFFX-r2-Bs-dap_5_signal28.201056
NoiseAvg:4.01,Std:0.12,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_signal10.237400
#P14041
Spike_AFFX-r2-Bs-phe_M_signal13.436914
Corner-Avg:10095,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal48.069653
Spike_AFFX-r2-Ec-bioB_3_signal38.230331
Spike_AFFX-r2-Bs-lys_M_signal9.316002
Spike_AFFX-r2-P1-cre_3_signal2509.427490
Spike_AFFX-r2-Bs-lys_3-5-ratio2.047812
Spike_AFFX-r2-Bs-dap_M_signal78.171692
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.646347
Spike_AFFX-r2-Ec-bioB_avg-signal40.723061
Spike_AFFX-r2-Bs-thr_avg-signal41.621639
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal397.049225
Spike_AFFX-r2-Bs-phe_5_signal14.892806
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal684.307556
RawQ3.404103
Spike_AFFX-r2-Bs-lys_5_signal7.105308
Signal(A)5.129985
%A36.540989
Signal(All)142.270065
Corner+Avg:172,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal168.029495
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.328892
Spike_AFFX-r2-Ec-bioD_avg-signal540.678406
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.556335
Spike_AFFX-r2-Bs-lys_avg-signal10.323882
Spike_AFFX-r2-P1-cre_avg-signal2294.271484
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.902674
Spike_AFFX-r2-Bs-thr_3_signal78.278709
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.886206
Spike_AFFX-r2-Bs-dap_3_signal105.602730
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.723483
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal163.858017
#M434
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal14.550336
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.025458
Spike_AFFX-r2-Bs-thr_M_signal36.348812
Signal(P)227.529434
Spike_AFFX-r2-Bs-phe_3-5-ratio1.902186
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8331,Count:9
Spike_AFFX-r2-P1-cre_5_signal2079.115723
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8335
Signal(M)17.698238
BackgroundAvg:88.31,Std:1.02,Min:86.0,Max:90.4
Spike_AFFX-r2-Ec-bioC_avg-signal165.943756
Spike_AFFX-r2-Bs-dap_avg-signal70.658485
Spike_AFFX-r2-Bs-dap_3-5-ratio3.744637
Spike_AFFX-r2-Ec-bioB_5_signal35.869194
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.448271
NF1.000000
HZ4
Tau0.015000

Slide: SEGUELA_593-5_pft1_0h_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 ("SEGUELA_593-5_pft1_0h_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: SEGUELA_593-5_pft1_0h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_129555 (BZ)
Stock Code: N629555
Genetic Background: Col-0 (Columbia, N60000)
Growth Conditions:
ProtocolCol-0 seedlings were grown on MS complemented with 0.5% Glucose for 7 days under continous light. After 7 days, seedlings were transfred in liquid culture in a Glucose free MS medium. After 24h, the medium was replaced by MS medium complemented with 3% Glucose. Seedlings were sampled after 6 hours of treatment.
Percentage Agrose10
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
LightingConstant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA Insertion
Tissue: whole plant
in vivo Treatment: 3% Glucose
Additional Organism Information:
Sample Description
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:0.472287
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-ratio1.088556
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.859663
Spike_AFFX-r2-Bs-dap_5_signal75.143967
NoiseAvg:3.45,Std:0.14,Min:3.1,Max:3.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal19.599716
#P14738
Spike_AFFX-r2-Bs-phe_M_signal24.157015
Corner-Avg:11500,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal72.265671
Spike_AFFX-r2-Ec-bioB_3_signal53.640408
Spike_AFFX-r2-Bs-lys_M_signal12.780397
Spike_AFFX-r2-P1-cre_3_signal2642.238770
Spike_AFFX-r2-Bs-lys_3-5-ratio1.966074
Spike_AFFX-r2-Bs-dap_M_signal159.019806
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.908581
Spike_AFFX-r2-Ec-bioB_avg-signal62.767712
Spike_AFFX-r2-Bs-thr_avg-signal57.752094
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal441.531952
Spike_AFFX-r2-Bs-phe_5_signal22.248159
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal773.377930
RawQ2.968313
Spike_AFFX-r2-Bs-lys_5_signal21.230862
Signal(A)4.302421
%A33.599300
Signal(All)141.419846
Corner+Avg:183,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal213.779785
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal25.575769
Spike_AFFX-r2-Ec-bioD_avg-signal607.454956
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.612015
Spike_AFFX-r2-Bs-lys_avg-signal25.250900
Spike_AFFX-r2-P1-cre_avg-signal2534.763184
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_signal96.206802
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal23.993647
Spike_AFFX-r2-Bs-dap_3_signal202.131317
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.751579
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal183.792557
#M408
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal41.741440
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.163158
Spike_AFFX-r2-Bs-thr_M_signal57.449768
Signal(P)216.214203
Spike_AFFX-r2-Bs-phe_3-5-ratio1.149568
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9964,Count:9
Spike_AFFX-r2-P1-cre_5_signal2427.287842
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7664
Signal(M)15.313145
BackgroundAvg:73.55,Std:0.51,Min:72.0,Max:75.3
Spike_AFFX-r2-Ec-bioC_avg-signal198.786163
Spike_AFFX-r2-Bs-dap_avg-signal145.431702
Spike_AFFX-r2-Bs-dap_3-5-ratio2.689921
Spike_AFFX-r2-Ec-bioB_5_signal62.397053
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.472287
NF1.000000
HZ4
Tau0.015000

Slide: SEGUELA_593-6_pft1_0h_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 ("SEGUELA_593-6_pft1_0h_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: SEGUELA_593-6_pft1_0h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_129555 (BZ)
Stock Code: N629555
Genetic Background: Col-0 (Columbia, N60000)
Growth Conditions:
ProtocolCol-0 seedlings were grown on MS complemented with 0.5% Glucose for 7 days under continous light. After 7 days, seedlings were transfred in liquid culture in a Glucose free MS medium. After 24h, the medium was replaced by MS medium complemented with 3% Glucose. Seedlings were sampled after 6 hours of treatment.
Percentage Agrose10
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
LightingConstant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA Insertion
Tissue: whole plant
in vivo Treatment: 3% Glucose
Additional Organism Information:
Sample Description
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:0.50203
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-ratio1.191743
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.721514
Spike_AFFX-r2-Bs-dap_5_signal54.654675
NoiseAvg:3.12,Std:0.05,Min:2.9,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal24.661463
#P14682
Spike_AFFX-r2-Bs-phe_M_signal15.724940
Corner-Avg:8276,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal52.661263
Spike_AFFX-r2-Ec-bioB_3_signal30.489712
Spike_AFFX-r2-Bs-lys_M_signal10.920377
Spike_AFFX-r2-P1-cre_3_signal2495.891113
Spike_AFFX-r2-Bs-lys_3-5-ratio2.236040
Spike_AFFX-r2-Bs-dap_M_signal128.232422
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.629376
Spike_AFFX-r2-Ec-bioB_avg-signal41.802979
Spike_AFFX-r2-Bs-thr_avg-signal47.341793
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal353.830627
Spike_AFFX-r2-Bs-phe_5_signal26.169647
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal568.333740
RawQ2.868285
Spike_AFFX-r2-Bs-lys_5_signal13.062194
Signal(A)4.446383
%A33.656292
Signal(All)138.909027
Corner+Avg:132,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal168.973785
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.239298
Spike_AFFX-r2-Ec-bioD_avg-signal461.082184
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.366508
Spike_AFFX-r2-Bs-lys_avg-signal17.730053
Spike_AFFX-r2-P1-cre_avg-signal2295.105957
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.977203
Spike_AFFX-r2-Bs-thr_3_signal64.844261
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal21.044628
Spike_AFFX-r2-Bs-dap_3_signal161.618820
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.606231
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal160.967911
#M451
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal29.207586
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.049736
Spike_AFFX-r2-Bs-thr_M_signal52.519653
Signal(P)212.988876
Spike_AFFX-r2-Bs-phe_3-5-ratio0.811600
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7244,Count:9
Spike_AFFX-r2-P1-cre_5_signal2094.320557
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7677
Signal(M)16.135632
BackgroundAvg:68.08,Std:0.65,Min:66.3,Max:70.0
Spike_AFFX-r2-Ec-bioC_avg-signal164.970856
Spike_AFFX-r2-Bs-dap_avg-signal114.835304
Spike_AFFX-r2-Bs-dap_3-5-ratio2.957091
Spike_AFFX-r2-Ec-bioB_5_signal42.257969
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.502030
NF1.000000
HZ4
Tau0.015000

Slide: SEGUELA_593-7_Col_6h_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 ("SEGUELA_593-7_Col_6h_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: SEGUELA_593-7_Col_6h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
ProtocolCol-0 seedlings were grown on MS complemented with 0.5% Glucose for 7 days under continous light. After 7 days, seedlings were transfred in liquid culture in a Glucose free MS medium. After 24h, the medium was replaced by MS medium complemented with 3% Glucose. Seedlings were sampled after 6 hours of treatment.
Percentage Agrose10
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
LightingConstant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
in vivo Treatment: 3% Glucose
Additional Organism Information:
Sample Description
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:0.37254
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-ratio1.046677
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.700659
Spike_AFFX-r2-Bs-dap_5_signal20.042418
NoiseAvg:3.76,Std:0.10,Min:3.3,Max:4.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal6.322240
#P15185
Spike_AFFX-r2-Bs-phe_M_signal8.461963
Corner-Avg:9536,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal46.372555
Spike_AFFX-r2-Ec-bioB_3_signal32.719147
Spike_AFFX-r2-Bs-lys_M_signal4.524007
Spike_AFFX-r2-P1-cre_3_signal2072.323730
Spike_AFFX-r2-Bs-lys_3-5-ratio2.500897
Spike_AFFX-r2-Bs-dap_M_signal47.603092
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.638557
Spike_AFFX-r2-Ec-bioB_avg-signal41.929806
Spike_AFFX-r2-Bs-thr_avg-signal22.089409
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal402.821960
Spike_AFFX-r2-Bs-phe_5_signal15.104580
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal538.828369
RawQ3.296542
Spike_AFFX-r2-Bs-lys_5_signal5.668322
Signal(A)3.542670
%A31.766769
Signal(All)137.162125
Corner+Avg:164,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal181.199417
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal13.147264
Spike_AFFX-r2-Ec-bioD_avg-signal470.825165
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.571678
Spike_AFFX-r2-Bs-lys_avg-signal8.122739
Spike_AFFX-r2-P1-cre_avg-signal2026.115356
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.661552
Spike_AFFX-r2-Bs-thr_3_signal29.326071
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal12.237935
Spike_AFFX-r2-Bs-dap_3_signal84.580505
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.337634
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal150.053986
#M379
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal14.175887
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.207561
Spike_AFFX-r2-Bs-thr_M_signal30.619911
Signal(P)203.989502
Spike_AFFX-r2-Bs-phe_3-5-ratio0.870416
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8132,Count:9
Spike_AFFX-r2-P1-cre_5_signal1979.906982
Spike_AFFX-r2-Bs-phe_M_detectionM
#A7246
Signal(M)14.293718
BackgroundAvg:84.55,Std:0.87,Min:82.5,Max:86.6
Spike_AFFX-r2-Ec-bioC_avg-signal165.626709
Spike_AFFX-r2-Bs-dap_avg-signal50.742004
Spike_AFFX-r2-Bs-dap_3-5-ratio4.220075
Spike_AFFX-r2-Ec-bioB_5_signal46.697704
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.372540
NF1.000000
HZ4
Tau0.015000

Slide: SEGUELA_593-8_Col_6h_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 ("SEGUELA_593-8_Col_6h_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: SEGUELA_593-8_Col_6h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
ProtocolCol-0 seedlings were grown on MS complemented with 0.5% Glucose for 7 days under continous light. After 7 days, seedlings were transfred in liquid culture in a Glucose free MS medium. After 24h, the medium was replaced by MS medium complemented with 3% Glucose. Seedlings were sampled after 6 hours of treatment.
Percentage Agrose10
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
LightingConstant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
in vivo Treatment: 3% Glucose
Additional Organism Information:
Sample Description
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:0.379008
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-ratio1.144570
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.834276
Spike_AFFX-r2-Bs-dap_5_signal33.174881
NoiseAvg:3.87,Std:0.12,Min:3.5,Max:4.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal15.226237
#P15266
Spike_AFFX-r2-Bs-phe_M_signal12.892325
Corner-Avg:11204,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal66.206078
Spike_AFFX-r2-Ec-bioB_3_signal42.022400
Spike_AFFX-r2-Bs-lys_M_signal12.805259
Spike_AFFX-r2-P1-cre_3_signal2967.365234
Spike_AFFX-r2-Bs-lys_3-5-ratio1.292030
Spike_AFFX-r2-Bs-dap_M_signal114.449471
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.018648
Spike_AFFX-r2-Ec-bioB_avg-signal52.866123
Spike_AFFX-r2-Bs-thr_avg-signal43.706985
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal555.889221
Spike_AFFX-r2-Bs-phe_5_signal12.498241
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal728.364929
RawQ3.405358
Spike_AFFX-r2-Bs-lys_5_signal13.193621
Signal(A)3.602185
%A31.424814
Signal(All)140.634995
Corner+Avg:193,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal201.353500
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.592398
Spike_AFFX-r2-Ec-bioD_avg-signal642.127075
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.926788
Spike_AFFX-r2-Bs-lys_avg-signal14.348477
Spike_AFFX-r2-P1-cre_avg-signal2779.961670
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_signal76.415123
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal15.660988
Spike_AFFX-r2-Bs-dap_3_signal99.289223
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.310270
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal174.132019
#M376
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal17.046556
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.156327
Spike_AFFX-r2-Bs-thr_M_signal39.479588
Signal(P)208.076355
Spike_AFFX-r2-Bs-phe_3-5-ratio1.727635
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8937,Count:9
Spike_AFFX-r2-P1-cre_5_signal2592.558105
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7168
Signal(M)14.813495
BackgroundAvg:82.72,Std:0.98,Min:79.6,Max:84.9
Spike_AFFX-r2-Ec-bioC_avg-signal187.742767
Spike_AFFX-r2-Bs-dap_avg-signal82.304527
Spike_AFFX-r2-Bs-dap_3-5-ratio2.992904
Spike_AFFX-r2-Ec-bioB_5_signal50.369892
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.379008
NF1.000000
HZ4
Tau0.015000

Slide: SEGUELA_593-9_Col_6h_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 ("SEGUELA_593-9_Col_6h_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: SEGUELA_593-9_Col_6h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
ProtocolCol-0 seedlings were grown on MS complemented with 0.5% Glucose for 7 days under continous light. After 7 days, seedlings were transfred in liquid culture in a Glucose free MS medium. After 24h, the medium was replaced by MS medium complemented with 3% Glucose. Seedlings were sampled after 6 hours of treatment.
Percentage Agrose10
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
LightingConstant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
in vivo Treatment: 3% Glucose
Additional Organism Information:
Sample Description
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:0.490227
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-ratio1.145075
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.762263
Spike_AFFX-r2-Bs-dap_5_signal21.073738
NoiseAvg:3.47,Std:0.14,Min:3.2,Max:4.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.703513
#P14832
Spike_AFFX-r2-Bs-phe_M_signal11.759146
Corner-Avg:8642,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal48.654480
Spike_AFFX-r2-Ec-bioB_3_signal31.516262
Spike_AFFX-r2-Bs-lys_M_signal6.181081
Spike_AFFX-r2-P1-cre_3_signal2359.320801
Spike_AFFX-r2-Bs-lys_3-5-ratio1.851787
Spike_AFFX-r2-Bs-dap_M_signal56.901932
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.412895
Spike_AFFX-r2-Ec-bioB_avg-signal40.505474
Spike_AFFX-r2-Bs-thr_avg-signal40.370586
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal391.047852
Spike_AFFX-r2-Bs-phe_5_signal17.081823
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal592.797424
RawQ3.126482
Spike_AFFX-r2-Bs-lys_5_signal8.618668
Signal(A)4.949644
%A33.095135
Signal(All)142.697189
Corner+Avg:150,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal189.378067
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal12.953372
Spike_AFFX-r2-Ec-bioD_avg-signal491.922638
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.024109
Spike_AFFX-r2-Bs-lys_avg-signal10.253230
Spike_AFFX-r2-P1-cre_avg-signal2209.864014
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.880754
Spike_AFFX-r2-Bs-thr_3_signal63.349884
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal13.931447
Spike_AFFX-r2-Bs-dap_3_signal97.230431
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.515920
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal184.959061
#M429
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal15.959940
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.023892
Spike_AFFX-r2-Bs-thr_M_signal46.058361
Signal(P)216.428345
Spike_AFFX-r2-Bs-phe_3-5-ratio0.758313
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7135,Count:9
Spike_AFFX-r2-P1-cre_5_signal2060.407227
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7549
Signal(M)17.465628
BackgroundAvg:73.20,Std:0.93,Min:71.1,Max:75.0
Spike_AFFX-r2-Ec-bioC_avg-signal187.168564
Spike_AFFX-r2-Bs-dap_avg-signal58.402027
Spike_AFFX-r2-Bs-dap_3-5-ratio4.613820
Spike_AFFX-r2-Ec-bioB_5_signal41.345669
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.490227
NF1.000000
HZ4
Tau0.015000

Slide: SEGUELA_593-10_pft1_6h_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 ("SEGUELA_593-10_pft1_6h_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: SEGUELA_593-10_pft1_6h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_129555 (BZ)
Stock Code: N629555
Genetic Background: Col-0 (Columbia, N60000)
Growth Conditions:
ProtocolCol-0 seedlings were grown on MS complemented with 0.5% Glucose for 7 days under continous light. After 7 days, seedlings were transfred in liquid culture in a Glucose free MS medium. After 24h, the medium was replaced by MS medium complemented with 3% Glucose. Seedlings were sampled after 6 hours of treatment.
Percentage Agrose10
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
LightingConstant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA Insertion
Tissue: whole plant
in vivo Treatment: 3% Glucose
Additional Organism Information:
Sample Description
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:0.501384
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-ratio1.298866
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.978312
Spike_AFFX-r2-Bs-dap_5_signal35.248650
NoiseAvg:3.15,Std:0.20,Min:2.8,Max:4.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal15.215823
#P14979
Spike_AFFX-r2-Bs-phe_M_signal19.541309
Corner-Avg:8901,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal63.223091
Spike_AFFX-r2-Ec-bioB_3_signal47.619946
Spike_AFFX-r2-Bs-lys_M_signal13.531626
Spike_AFFX-r2-P1-cre_3_signal3110.722900
Spike_AFFX-r2-Bs-lys_3-5-ratio1.547920
Spike_AFFX-r2-Bs-dap_M_signal87.325966
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.873662
Spike_AFFX-r2-Ec-bioB_avg-signal53.172894
Spike_AFFX-r2-Bs-thr_avg-signal51.498020
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal455.889008
Spike_AFFX-r2-Bs-phe_5_signal19.698446
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal630.607849
RawQ2.838768
Spike_AFFX-r2-Bs-lys_5_signal10.131020
Signal(A)3.674588
%A32.626041
Signal(All)138.797104
Corner+Avg:145,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal225.291077
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal29.042328
Spike_AFFX-r2-Ec-bioD_avg-signal543.248413
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.668564
Spike_AFFX-r2-Bs-lys_avg-signal13.114883
Spike_AFFX-r2-P1-cre_avg-signal2752.837891
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.705392
Spike_AFFX-r2-Bs-thr_3_signal89.372597
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal22.760695
Spike_AFFX-r2-Bs-dap_3_signal142.400238
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.383249
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal206.284836
#M389
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal15.682004
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.092136
Spike_AFFX-r2-Bs-thr_M_signal49.905643
Signal(P)209.176620
Spike_AFFX-r2-Bs-phe_3-5-ratio1.474346
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6864,Count:9
Spike_AFFX-r2-P1-cre_5_signal2394.952881
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7442
Signal(M)13.776392
BackgroundAvg:68.46,Std:0.49,Min:67.2,Max:69.8
Spike_AFFX-r2-Ec-bioC_avg-signal215.787964
Spike_AFFX-r2-Bs-dap_avg-signal88.324951
Spike_AFFX-r2-Bs-dap_3-5-ratio4.039878
Spike_AFFX-r2-Ec-bioB_5_signal48.675636
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.501384
NF1.000000
HZ4
Tau0.015000

Slide: SEGUELA_593-11_pft1_6h_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 ("SEGUELA_593-11_pft1_6h_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: SEGUELA_593-11_pft1_6h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_129555 (BZ)
Stock Code: N629555
Genetic Background: Col-0 (Columbia, N60000)
Growth Conditions:
ProtocolCol-0 seedlings were grown on MS complemented with 0.5% Glucose for 7 days under continous light. After 7 days, seedlings were transfred in liquid culture in a Glucose free MS medium. After 24h, the medium was replaced by MS medium complemented with 3% Glucose. Seedlings were sampled after 6 hours of treatment.
Percentage Agrose10
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
LightingConstant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA Insertion
Tissue: whole plant
in vivo Treatment: 3% Glucose
Additional Organism Information:
Sample Description
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:0.454099
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-ratio1.293422
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.994266
Spike_AFFX-r2-Bs-dap_5_signal19.974903
NoiseAvg:3.06,Std:0.09,Min:2.8,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.987977
#P15550
Spike_AFFX-r2-Bs-phe_M_signal8.943216
Corner-Avg:8222,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal42.387032
Spike_AFFX-r2-Ec-bioB_3_signal41.274849
Spike_AFFX-r2-Bs-lys_M_signal5.422216
Spike_AFFX-r2-P1-cre_3_signal2701.045410
Spike_AFFX-r2-Bs-lys_3-5-ratio2.231614
Spike_AFFX-r2-Bs-dap_M_signal46.901726
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.658145
Spike_AFFX-r2-Ec-bioB_avg-signal41.724926
Spike_AFFX-r2-Bs-thr_avg-signal27.651354
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal378.868713
Spike_AFFX-r2-Bs-phe_5_signal9.899571
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal515.121399
RawQ2.782075
Spike_AFFX-r2-Bs-lys_5_signal6.324215
Signal(A)3.315172
%A30.267427
Signal(All)136.724152
Corner+Avg:135,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal166.850769
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal9.559020
Spike_AFFX-r2-Ec-bioD_avg-signal446.995056
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.171852
Spike_AFFX-r2-Bs-lys_avg-signal8.619880
Spike_AFFX-r2-P1-cre_avg-signal2394.669922
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.560719
Spike_AFFX-r2-Bs-thr_3_signal41.867306
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-signal9.467269
Spike_AFFX-r2-Bs-dap_3_signal79.379852
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.359630
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal154.038239
#M356
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal14.113209
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.083178
Spike_AFFX-r2-Bs-thr_M_signal32.098782
Signal(P)198.811096
Spike_AFFX-r2-Bs-phe_3-5-ratio0.965599
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6832,Count:9
Spike_AFFX-r2-P1-cre_5_signal2088.294189
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6904
Signal(M)12.015474
BackgroundAvg:68.88,Std:0.55,Min:67.1,Max:70.5
Spike_AFFX-r2-Ec-bioC_avg-signal160.444504
Spike_AFFX-r2-Bs-dap_avg-signal48.752163
Spike_AFFX-r2-Bs-dap_3-5-ratio3.973979
Spike_AFFX-r2-Ec-bioB_5_signal41.512890
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.454099
NF1.000000
HZ4
Tau0.015000

Slide: SEGUELA_593-12_pft1_6h_Rep3_ATH1

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

Summary Information

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

  • Extract 1 ("SEGUELA_593-12_pft1_6h_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: SEGUELA_593-12_pft1_6h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_129555 (BZ)
Stock Code: N629555
Genetic Background: Col-0 (Columbia, N60000)
Growth Conditions:
ProtocolCol-0 seedlings were grown on MS complemented with 0.5% Glucose for 7 days under continous light. After 7 days, seedlings were transfred in liquid culture in a Glucose free MS medium. After 24h, the medium was replaced by MS medium complemented with 3% Glucose. Seedlings were sampled after 6 hours of treatment.
Percentage Agrose10
Temperature22 °C average, 22 °C day, 22 °C night
Humidity70 % average, 70 % day, 70 % night
Medium
LightingConstant light
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA Insertion
Tissue: whole plant
in vivo Treatment: 3% Glucose
Additional Organism Information:
Sample Description
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:0.362338
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-ratio1.427178
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.784709
Spike_AFFX-r2-Bs-dap_5_signal53.013283
NoiseAvg:3.42,Std:0.10,Min:3.2,Max:3.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal25.222170
#P15773
Spike_AFFX-r2-Bs-phe_M_signal15.910068
Corner-Avg:9979,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal52.611496
Spike_AFFX-r2-Ec-bioB_3_signal37.328106
Spike_AFFX-r2-Bs-lys_M_signal13.388618
Spike_AFFX-r2-P1-cre_3_signal3040.224365
Spike_AFFX-r2-Bs-lys_3-5-ratio2.366303
Spike_AFFX-r2-Bs-dap_M_signal153.816101
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.408082
Spike_AFFX-r2-Ec-bioB_avg-signal45.836323
Spike_AFFX-r2-Bs-thr_avg-signal53.383144
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal470.446655
Spike_AFFX-r2-Bs-phe_5_signal27.030645
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal577.892883
RawQ3.018991
Spike_AFFX-r2-Bs-lys_5_signal13.847380
Signal(A)2.954004
%A29.316090
Signal(All)136.487244
Corner+Avg:168,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal194.570389
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal29.028034
Spike_AFFX-r2-Ec-bioD_avg-signal524.169800
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.149498
Spike_AFFX-r2-Bs-lys_avg-signal20.001032
Spike_AFFX-r2-P1-cre_avg-signal2585.229492
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.534415
Spike_AFFX-r2-Bs-thr_3_signal85.959221
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal23.989584
Spike_AFFX-r2-Bs-dap_3_signal128.033051
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.228392
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal183.870636
#M350
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal32.767097
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.058192
Spike_AFFX-r2-Bs-thr_M_signal48.968044
Signal(P)195.847900
Spike_AFFX-r2-Bs-phe_3-5-ratio1.073894
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7767,Count:9
Spike_AFFX-r2-P1-cre_5_signal2130.234375
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6687
Signal(M)12.605062
BackgroundAvg:78.66,Std:0.90,Min:75.4,Max:80.0
Spike_AFFX-r2-Ec-bioC_avg-signal189.220520
Spike_AFFX-r2-Bs-dap_avg-signal111.620811
Spike_AFFX-r2-Bs-dap_3-5-ratio2.415113
Spike_AFFX-r2-Ec-bioB_5_signal47.569366
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.362338
NF1.000000
HZ4
Tau0.015000


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