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Experiment: Ethylene signaling enhances salt tolerance in Arabidopsis thaliana

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-659

Ethylene has been regarded as a stress hormone to regulate myriad stress responses. But how ethylene signaling is involved in the salt stress is poorly understood. To dissect the underlying molecular mechanisms, we performed transcriptome profiling of transgenic plants overexpressing EIN3 (EIN3ox), ein3eil1 double mutant and wild type Col-0. EIN3 and EIL1 are two key transcription factors in ethylene signaling pathway. For this analysis, 5-d-old seedlings treated with or without 200 mM NaCl for 6 h were used for RNA preparation. This design enabled us to examine the overlap in expression pattern among these plants, as well as to identify salt-induced and EIN3/EIL1-dependent genes.

About the Experimenter

Name:Dr. Zhonghai Li
Head of Lab Name:Professor Hongwei Guo
Lab:
Address:College of Life Sciences
Peking University
Beijing, 100871
P.R.China
Postcode: 100871
Country: P.R.China
 

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: growth_condition_design;
Number of Slides:6
 
Experimental Parameters:
parameterSalt stress
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Li: Ethylene signaling enhances salt tolerance in Arabidopsis thaliana

Slide: Li_659-Col-0_Control_Rep_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 ("Li_659-Col-0_Control_Rep_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: Li_659-Col-0_Control_Rep_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: CS6673
Growth Conditions:
Stratification4 degree C for 3 days
Sterilisation75% ethanol with 0.05% triton X-100 for 10 min, 100% ethanol for 1 min
ProtocolSeeds were placed on MS medium and allowed to grow for 5 days, 16L/8D, 22 degree C
Percentage Agrose0.8
Substrate Sterilising Procedure120 degree for 20 min
Plant Spacingabout 250 seedlings per plate
Temperature22 °C average, 22 °C day, 22 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
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:0.876011
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-ratio1.285482
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.287741
Spike_AFFX-r2-Bs-dap_5_signal213.199066
NoiseAvg:2.66,Std:0.08,Min:2.4,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal33.028488
#P12835
Spike_AFFX-r2-Bs-phe_M_signal69.489929
Corner-Avg:17177,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal124.100380
Spike_AFFX-r2-Ec-bioB_3_signal133.892990
Spike_AFFX-r2-Bs-lys_M_signal36.427197
Spike_AFFX-r2-P1-cre_3_signal5872.276855
Spike_AFFX-r2-Bs-lys_3-5-ratio1.584510
Spike_AFFX-r2-Bs-dap_M_signal437.573273
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.067528
Spike_AFFX-r2-Ec-bioB_avg-signal120.656158
Spike_AFFX-r2-Bs-thr_avg-signal96.235512
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1150.729126
Spike_AFFX-r2-Bs-phe_5_signal93.753632
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1681.278442
RawQ2.971303
Spike_AFFX-r2-Bs-lys_5_signal27.861471
Signal(A)6.145166
%A41.306446
Signal(All)155.330261
Corner+Avg:126,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal298.328888
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal85.417831
Spike_AFFX-r2-Ec-bioD_avg-signal1416.003784
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P56.269180
Spike_AFFX-r2-Bs-lys_avg-signal36.145153
Spike_AFFX-r2-P1-cre_avg-signal5220.214355
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.424375
Spike_AFFX-r2-Bs-thr_3_signal167.372803
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-signal82.887131
Spike_AFFX-r2-Bs-dap_3_signal371.072021
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.461055
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal346.262146
#M553
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal44.146793
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.861569
Spike_AFFX-r2-Bs-thr_M_signal88.305229
Signal(P)270.719360
Spike_AFFX-r2-Bs-phe_3-5-ratio0.911088
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:17162,Count:9
Spike_AFFX-r2-P1-cre_5_signal4568.151855
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9422
Signal(M)18.988173
BackgroundAvg:70.85,Std:0.57,Min:69.6,Max:72.7
Spike_AFFX-r2-Ec-bioC_avg-signal322.295532
Spike_AFFX-r2-Bs-dap_avg-signal340.614777
Spike_AFFX-r2-Bs-dap_3-5-ratio1.740496
Spike_AFFX-r2-Ec-bioB_5_signal103.975098
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.876011
NF1.000000
HZ4
Tau0.015000

Slide: Li_659-Col-0_NaCl_Rep_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 ("Li_659-Col-0_NaCl_Rep_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: Li_659-Col-0_NaCl_Rep_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: CS6673
Growth Conditions:
Stratification4 degree C for 3 days
Sterilisation75% ethanol with 0.05% triton X-100 for 10 min, 100% ethanol for 1 min
ProtocolSeeds were placed on MS medium and allowed to grow for 5 days, 16L/8D, 22 degree C
Percentage Agrose0.8
Substrate Sterilising Procedure120 degree for 20 min
Plant Spacingabout 250 seedlings per plate
Temperature22 °C average, 22 °C day, 22 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
Additional Organism Information:
Sample Description5-d-old seedlings are treated with 200 mM NaCl for 6 hours
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:0.920919
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-ratio1.585268
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.216553
Spike_AFFX-r2-Bs-dap_5_signal80.189362
NoiseAvg:3.19,Std:0.14,Min:3.0,Max:3.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal17.628630
#P13284
Spike_AFFX-r2-Bs-phe_M_signal42.908630
Corner-Avg:17736,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal111.736160
Spike_AFFX-r2-Ec-bioB_3_signal100.503120
Spike_AFFX-r2-Bs-lys_M_signal23.041576
Spike_AFFX-r2-P1-cre_3_signal5160.458496
Spike_AFFX-r2-Bs-lys_3-5-ratio2.011783
Spike_AFFX-r2-Bs-dap_M_signal183.588272
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.891997
Spike_AFFX-r2-Ec-bioB_avg-signal98.284096
Spike_AFFX-r2-Bs-thr_avg-signal44.107685
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1021.063843
Spike_AFFX-r2-Bs-phe_5_signal38.468929
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1183.601196
RawQ3.445485
Spike_AFFX-r2-Bs-lys_5_signal15.266086
Signal(A)6.428726
%A39.530907
Signal(All)146.649826
Corner+Avg:133,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal249.699081
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal38.756630
Spike_AFFX-r2-Ec-bioD_avg-signal1102.332520
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.237614
Spike_AFFX-r2-Bs-lys_avg-signal23.006571
Spike_AFFX-r2-P1-cre_avg-signal4207.858398
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.231477
Spike_AFFX-r2-Bs-thr_3_signal68.610573
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal40.044727
Spike_AFFX-r2-Bs-dap_3_signal174.534302
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.159184
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal237.679550
#M509
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal30.712051
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.050570
Spike_AFFX-r2-Bs-thr_M_signal46.083855
Signal(P)246.672440
Spike_AFFX-r2-Bs-phe_3-5-ratio1.007479
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14651,Count:9
Spike_AFFX-r2-P1-cre_5_signal3255.258301
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9017
Signal(M)20.270744
BackgroundAvg:82.15,Std:1.01,Min:80.1,Max:84.7
Spike_AFFX-r2-Ec-bioC_avg-signal243.689316
Spike_AFFX-r2-Bs-dap_avg-signal146.103973
Spike_AFFX-r2-Bs-dap_3-5-ratio2.176527
Spike_AFFX-r2-Ec-bioB_5_signal82.612991
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.920919
NF1.000000
HZ4
Tau0.015000

Slide: Li_659-ein3eil1_Control_Rep_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 ("Li_659-ein3eil1_Control_Rep_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: Li_659-ein3eil1_Control_Rep_ATH1
Organism: Arabidopsis thaliana
Alias: ethylene insensitive
Stock Code: CS8052
Genetic Background: Col
Growth Conditions:
Stratification4 degree C for 3 days
Sterilisation75% ethanol with 0.05% triton X-100 for 10 min, 100% ethanol for 1 min
ProtocolSeeds were placed on MS medium and allowed to grow for 5 days, 16L/8D, 22 degree C
Percentage Agrose0.8
Substrate Sterilising Procedure120 degree for 20 min
Plant Spacingabout 250 seedlings per plate
Temperature22 °C average, 22 °C day, 22 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: Single marker
Tissue: whole plant
Additional Organism Information:
Sample Description5-d-old seedlings are treated with 200 mM NaCl for 6 hours
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:0.970688
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-ratio1.911248
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.213173
Spike_AFFX-r2-Bs-dap_5_signal93.752014
NoiseAvg:3.38,Std:0.09,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_signal12.948080
#P13009
Spike_AFFX-r2-Bs-phe_M_signal33.064739
Corner-Avg:17725,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal123.161118
Spike_AFFX-r2-Ec-bioB_3_signal100.686203
Spike_AFFX-r2-Bs-lys_M_signal18.429932
Spike_AFFX-r2-P1-cre_3_signal6440.554688
Spike_AFFX-r2-Bs-lys_3-5-ratio0.669704
Spike_AFFX-r2-Bs-dap_M_signal205.668396
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.128886
Spike_AFFX-r2-Ec-bioB_avg-signal102.280479
Spike_AFFX-r2-Bs-thr_avg-signal41.613541
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1257.668823
Spike_AFFX-r2-Bs-phe_5_signal46.866928
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1520.804932
RawQ3.832820
Spike_AFFX-r2-Bs-lys_5_signal24.923714
Signal(A)7.922994
%A40.745289
Signal(All)148.644775
Corner+Avg:132,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal350.133240
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal42.858788
Spike_AFFX-r2-Ec-bioD_avg-signal1389.236816
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.032005
Spike_AFFX-r2-Bs-lys_avg-signal20.015051
Spike_AFFX-r2-P1-cre_avg-signal4905.185547
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.222709
Spike_AFFX-r2-Bs-thr_3_signal66.409225
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal40.930149
Spike_AFFX-r2-Bs-dap_3_signal171.422516
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.209225
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal286.978271
#M507
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal16.691507
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.220069
Spike_AFFX-r2-Bs-thr_M_signal45.483315
Signal(P)254.027130
Spike_AFFX-r2-Bs-phe_3-5-ratio0.914478
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16217,Count:9
Spike_AFFX-r2-P1-cre_5_signal3369.816406
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9294
Signal(M)24.284218
BackgroundAvg:99.16,Std:0.61,Min:97.7,Max:100.8
Spike_AFFX-r2-Ec-bioC_avg-signal318.555756
Spike_AFFX-r2-Bs-dap_avg-signal156.947647
Spike_AFFX-r2-Bs-dap_3-5-ratio1.828468
Spike_AFFX-r2-Ec-bioB_5_signal82.994110
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.970688
NF1.000000
HZ4
Tau0.015000

Slide: Li_659-ein3eil1_NaCl_Rep_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 ("Li_659-ein3eil1_NaCl_Rep_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: Li_659-ein3eil1_NaCl_Rep_ATH1
Organism: Arabidopsis thaliana
Alias: ethylene insensitive
Stock Code: CS8052
Genetic Background: Col
Growth Conditions:
Stratification4 degree C for 3 days
Sterilisation75% ethanol with 0.05% triton X-100 for 10 min, 100% ethanol for 1 min
ProtocolSeeds were placed on MS medium and allowed to grow for 5 days, 16L/8D, 22 degree C
Percentage Agrose0.8
Substrate Sterilising Procedure120 degree for 20 min
Plant Spacingabout 250 seedlings per plate
Temperature22 °C average, 22 °C day, 22 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: Single marker
Tissue: whole plant
Additional Organism Information:
Sample Description5-d-old seedlings are treated with 200 mM NaCl for 6 hours
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:1.07211
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-ratio1.496333
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.976743
Spike_AFFX-r2-Bs-dap_5_signal113.449799
NoiseAvg:3.36,Std:0.28,Min:2.8,Max:4.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal35.058586
#P12495
Spike_AFFX-r2-Bs-phe_M_signal39.672787
Corner-Avg:16557,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal121.315323
Spike_AFFX-r2-Ec-bioB_3_signal79.519897
Spike_AFFX-r2-Bs-lys_M_signal20.507368
Spike_AFFX-r2-P1-cre_3_signal5386.146484
Spike_AFFX-r2-Bs-lys_3-5-ratio1.093296
Spike_AFFX-r2-Bs-dap_M_signal234.920929
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.999110
Spike_AFFX-r2-Ec-bioB_avg-signal94.082848
Spike_AFFX-r2-Bs-thr_avg-signal74.031120
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1106.154907
Spike_AFFX-r2-Bs-phe_5_signal31.444511
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1442.494019
RawQ3.698515
Spike_AFFX-r2-Bs-lys_5_signal16.941006
Signal(A)7.292166
%A42.959229
Signal(All)146.106369
Corner+Avg:125,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal337.303741
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal60.183575
Spike_AFFX-r2-Ec-bioD_avg-signal1274.324463
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P54.778606
Spike_AFFX-r2-Bs-lys_avg-signal18.656637
Spike_AFFX-r2-P1-cre_avg-signal4492.854980
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.262166
Spike_AFFX-r2-Bs-thr_3_signal140.203140
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal43.766956
Spike_AFFX-r2-Bs-dap_3_signal197.025269
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.304062
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal233.526077
#M516
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.521540
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.444394
Spike_AFFX-r2-Bs-thr_M_signal46.831615
Signal(P)260.053772
Spike_AFFX-r2-Bs-phe_3-5-ratio1.913961
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14013,Count:9
Spike_AFFX-r2-P1-cre_5_signal3599.563721
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9799
Signal(M)22.981474
BackgroundAvg:87.61,Std:1.54,Min:83.3,Max:91.5
Spike_AFFX-r2-Ec-bioC_avg-signal285.414917
Spike_AFFX-r2-Bs-dap_avg-signal181.798660
Spike_AFFX-r2-Bs-dap_3-5-ratio1.736674
Spike_AFFX-r2-Ec-bioB_5_signal81.413315
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.072110
NF1.000000
HZ4
Tau0.015000

Slide: Li_659-EIN3ox_Control_Rep_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 ("Li_659-EIN3ox_Control_Rep_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: Li_659-EIN3ox_Control_Rep_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
Stratification4 degree C for 3 days
Sterilisation75% ethanol with 0.05% triton X-100 for 10 min, 100% ethanol for 1 min
ProtocolSeeds were placed on MS medium and allowed to grow for 5 days, 16L/8D, 22 degree C
Percentage Agrose0.8
Substrate Sterilising Procedure120 degree for 20 min
Plant Spacingabout 250 seedlings per plate
Temperature22 °C average, 22 °C day, 22 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
Additional Organism Information:
Sample Description5-d-old seedlings are treated with 200 mM NaCl for 6 hours
Other Information:
ecotype_habitat

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:0.978772
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-ratio1.413201
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.396789
Spike_AFFX-r2-Bs-dap_5_signal176.076019
NoiseAvg:2.80,Std:0.08,Min:2.5,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal31.508404
#P13138
Spike_AFFX-r2-Bs-phe_M_signal72.896072
Corner-Avg:16906,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal147.867401
Spike_AFFX-r2-Ec-bioB_3_signal152.886017
Spike_AFFX-r2-Bs-lys_M_signal31.206341
Spike_AFFX-r2-P1-cre_3_signal5680.437500
Spike_AFFX-r2-Bs-lys_3-5-ratio1.377228
Spike_AFFX-r2-Bs-dap_M_signal383.612854
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.969739
Spike_AFFX-r2-Ec-bioB_avg-signal136.736252
Spike_AFFX-r2-Bs-thr_avg-signal97.011086
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1206.461548
Spike_AFFX-r2-Bs-phe_5_signal60.274952
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1657.761230
RawQ3.116528
Spike_AFFX-r2-Bs-lys_5_signal39.144650
Signal(A)6.748232
%A40.026306
Signal(All)152.049438
Corner+Avg:139,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal309.823883
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal67.642700
Spike_AFFX-r2-Ec-bioD_avg-signal1432.111328
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.597546
Spike_AFFX-r2-Bs-lys_avg-signal41.420696
Spike_AFFX-r2-P1-cre_avg-signal4849.996094
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.376151
Spike_AFFX-r2-Bs-thr_3_signal156.588562
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-signal66.937904
Spike_AFFX-r2-Bs-dap_3_signal334.499268
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.374069
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal327.496979
#M542
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal53.911095
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.946036
Spike_AFFX-r2-Bs-thr_M_signal102.936310
Signal(P)258.414307
Spike_AFFX-r2-Bs-phe_3-5-ratio1.122236
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15766,Count:9
Spike_AFFX-r2-P1-cre_5_signal4019.554932
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9130
Signal(M)21.382004
BackgroundAvg:73.14,Std:0.57,Min:72.0,Max:74.4
Spike_AFFX-r2-Ec-bioC_avg-signal318.660431
Spike_AFFX-r2-Bs-dap_avg-signal298.062714
Spike_AFFX-r2-Bs-dap_3-5-ratio1.899743
Spike_AFFX-r2-Ec-bioB_5_signal109.455360
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.978772
NF1.000000
HZ4
Tau0.015000

Slide: Li_659-EIN3ox_NaCl_Rep_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 ("Li_659-EIN3ox_NaCl_Rep_ATH1") was made from "" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Li_659-EIN3ox_NaCl_Rep_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.351889
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-ratio1.119799
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.269653
Spike_AFFX-r2-Bs-dap_5_signal164.433014
NoiseAvg:2.19,Std:0.06,Min:2.1,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal29.176529
#P12452
Spike_AFFX-r2-Bs-phe_M_signal66.387779
Corner-Avg:17030,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal172.943649
Spike_AFFX-r2-Ec-bioB_3_signal147.127808
Spike_AFFX-r2-Bs-lys_M_signal37.915268
Spike_AFFX-r2-P1-cre_3_signal5543.661621
Spike_AFFX-r2-Bs-lys_3-5-ratio0.955165
Spike_AFFX-r2-Bs-dap_M_signal424.284271
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.720013
Spike_AFFX-r2-Ec-bioB_avg-signal145.317261
Spike_AFFX-r2-Bs-thr_avg-signal111.580711
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1228.837646
Spike_AFFX-r2-Bs-phe_5_signal92.368912
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1691.193848
RawQ2.804749
Spike_AFFX-r2-Bs-lys_5_signal45.666119
Signal(A)6.858891
%A43.147743
Signal(All)147.795731
Corner+Avg:124,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal371.371490
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal123.915688
Spike_AFFX-r2-Ec-bioD_avg-signal1460.015747
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P54.590092
Spike_AFFX-r2-Bs-lys_avg-signal42.400024
Spike_AFFX-r2-P1-cre_avg-signal5247.124512
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.262166
Spike_AFFX-r2-Bs-thr_3_signal196.066650
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-signal94.224121
Spike_AFFX-r2-Bs-dap_3_signal394.991272
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.376255
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal307.938507
#M516
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal43.618690
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.205992
Spike_AFFX-r2-Bs-thr_M_signal109.498940
Signal(P)264.355011
Spike_AFFX-r2-Bs-phe_3-5-ratio1.341530
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15890,Count:9
Spike_AFFX-r2-P1-cre_5_signal4950.587402
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9842
Signal(M)23.190889
BackgroundAvg:66.06,Std:0.48,Min:64.9,Max:67.2
Spike_AFFX-r2-Ec-bioC_avg-signal339.654999
Spike_AFFX-r2-Bs-dap_avg-signal327.902832
Spike_AFFX-r2-Bs-dap_3-5-ratio2.402141
Spike_AFFX-r2-Ec-bioB_5_signal115.880295
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.351889
NF1.000000
HZ4
Tau0.015000


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