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Experiment: Hydrogen peroxide and light treatment

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-576

Plant7days arabidopsis seedlingscontrol was grown in the darkHP was grown in the dark and treated with H2O2light was grown in the light.each sample has 2 biological replicates.

About the Experimenter

Name: Han Cheng
Head of Lab Name:Prof Dianjing Guo
Lab:
Address:Department of Biology, Faculty of Science, Chinese University of Hong Kong
Science Centre, Shatin, New Territories, Hong Kong, , HONG KONG
Postcode:
Country:
 
Telephone Number: 00852 26961258
Fax Number: (852) 2603-5646

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

About this Experiment

Experiment Type: compound_based_treatment
Number of Slides:6
 
Experimental Parameters:
parametercompound_based_treatment
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Cheng: Hydrogen peroxide and light treatment

Slide: Cheng_576-1_7-day_dark_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 ("Cheng_576-1_7-day_dark_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: Cheng_576-1_7-day_dark_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: col-0
Stock Code:
Growth Conditions:
Stratificationthe seeds were sterilised in 50% bleach containing 0.02% Tween-20 for 10 min, then washed 5 times with distilled water. The seeds were dried on filter paper and sprinkled onto 1/2 MS agar plate.
Sterilisation4 degree in refrigerator for 2 days.
Protocol
Substrate Sterilising Procedureautoclave
Temperature22 °C average, 22 °C day, 22 °C night
Humidity80 % average, 80 % day, 80 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: None. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: 5 mM hydrogen peroxide was added into media from the beginning.
Additional Organism Information:
Sample DescriptionThe whole seedlings were collected in the green safe light (Green LED lamp, wavelength 520~540 nm) and frozened in LN.
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:0.589528
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-ratio1.149342
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.116629
Spike_AFFX-r2-Bs-dap_5_signal114.253784
NoiseAvg:2.40,Std:0.08,Min:2.2,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal52.817417
#P15107
Spike_AFFX-r2-Bs-phe_M_signal69.976974
Corner-Avg:12663,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal170.836502
Spike_AFFX-r2-Ec-bioB_3_signal117.835854
Spike_AFFX-r2-Bs-lys_M_signal37.618050
Spike_AFFX-r2-P1-cre_3_signal5898.067871
Spike_AFFX-r2-Bs-lys_3-5-ratio0.952367
Spike_AFFX-r2-Bs-dap_M_signal351.862274
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.623443
Spike_AFFX-r2-Ec-bioB_avg-signal131.400177
Spike_AFFX-r2-Bs-thr_avg-signal185.879822
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1233.817505
Spike_AFFX-r2-Bs-phe_5_signal84.886940
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1821.991699
RawQ2.368065
Spike_AFFX-r2-Bs-lys_5_signal58.065781
Signal(A)3.430094
%A31.999123
Signal(All)143.622147
Corner+Avg:186,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal405.463257
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal102.206558
Spike_AFFX-r2-Ec-bioD_avg-signal1527.904541
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.229721
Spike_AFFX-r2-Bs-lys_avg-signal50.327923
Spike_AFFX-r2-P1-cre_avg-signal5514.880371
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.771153
Spike_AFFX-r2-Bs-thr_3_signal349.833160
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-signal85.690155
Spike_AFFX-r2-Bs-dap_3_signal607.436401
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.476711
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal411.320770
#M404
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal55.299942
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.985759
Spike_AFFX-r2-Bs-thr_M_signal154.988892
Signal(P)214.893188
Spike_AFFX-r2-Bs-phe_3-5-ratio1.204032
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8590,Count:9
Spike_AFFX-r2-P1-cre_5_signal5131.692871
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7299
Signal(M)11.369440
BackgroundAvg:57.32,Std:0.49,Min:56.4,Max:58.7
Spike_AFFX-r2-Ec-bioC_avg-signal408.392029
Spike_AFFX-r2-Bs-dap_avg-signal357.850830
Spike_AFFX-r2-Bs-dap_3-5-ratio5.316554
Spike_AFFX-r2-Ec-bioB_5_signal105.528160
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.589528
NF1.000000
HZ4
Tau0.015000

Slide: Cheng_576-2_7-day_dark_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 ("Cheng_576-2_7-day_dark_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: Cheng_576-2_7-day_dark_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: col-0
Stock Code:
Growth Conditions:
Stratificationthe seeds were sterilised in 50% bleach containing 0.02% Tween-20 for 10 min, then washed 5 times with distilled water. The seeds were dried on filter paper and sprinkled onto 1/2 MS agar plate.
Sterilisation4 degree in refrigerator for 2 days.
Protocol
Substrate Sterilising Procedureautoclave
Temperature22 °C average, 22 °C day, 22 °C night
Humidity80 % average, 80 % day, 80 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: None. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: 5 mM hydrogen peroxide was added into media from the beginning.
Additional Organism Information:
Sample DescriptionThe whole seedlings were collected in the green safe light (Green LED lamp, wavelength 520~540 nm) and frozened in LN.
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:0.968977
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-ratio1.082994
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.186410
Spike_AFFX-r2-Bs-dap_5_signal308.872864
NoiseAvg:1.76,Std:0.06,Min:1.6,Max:1.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal136.720810
#P14226
Spike_AFFX-r2-Bs-phe_M_signal120.448563
Corner-Avg:12261,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal263.910217
Spike_AFFX-r2-Ec-bioB_3_signal190.350952
Spike_AFFX-r2-Bs-lys_M_signal63.239361
Spike_AFFX-r2-P1-cre_3_signal7520.767578
Spike_AFFX-r2-Bs-lys_3-5-ratio0.979437
Spike_AFFX-r2-Bs-dap_M_signal666.823303
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.172950
Spike_AFFX-r2-Ec-bioB_avg-signal204.901321
Spike_AFFX-r2-Bs-thr_avg-signal351.692993
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1699.564575
Spike_AFFX-r2-Bs-phe_5_signal126.146774
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2645.874268
RawQ1.896286
Spike_AFFX-r2-Bs-lys_5_signal94.103264
Signal(A)3.972398
%A35.681717
Signal(All)148.370087
Corner+Avg:175,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal606.784668
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal158.346024
Spike_AFFX-r2-Ec-bioD_avg-signal2172.719482
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.367382
Spike_AFFX-r2-Bs-lys_avg-signal83.170265
Spike_AFFX-r2-P1-cre_avg-signal7232.596680
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.950899
Spike_AFFX-r2-Bs-thr_3_signal570.529053
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-signal134.980453
Spike_AFFX-r2-Bs-dap_3_signal960.115051
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.556795
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal694.404480
#M445
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal92.168182
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.873820
Spike_AFFX-r2-Bs-thr_M_signal347.829132
Signal(P)235.149323
Spike_AFFX-r2-Bs-phe_3-5-ratio1.255252
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9651,Count:9
Spike_AFFX-r2-P1-cre_5_signal6944.425293
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8139
Signal(M)15.182179
BackgroundAvg:46.33,Std:0.42,Min:45.4,Max:47.4
Spike_AFFX-r2-Ec-bioC_avg-signal650.594604
Spike_AFFX-r2-Bs-dap_avg-signal645.270447
Spike_AFFX-r2-Bs-dap_3-5-ratio3.108447
Spike_AFFX-r2-Ec-bioB_5_signal160.442810
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.968977
NF1.000000
HZ4
Tau0.015000

Slide: Cheng_576-3_7-days_H2O2 _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 ("Cheng_576-3_7-days_H2O2 _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: Cheng_576-3_7-days_H2O2 _Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: col-0
Stock Code:
Growth Conditions:
Stratificationthe seeds were sterilised in 50% bleach containing 0.02% Tween-20 for 10 min, then washed 5 times with distilled water. The seeds were dried on filter paper and sprinkled onto 1/2 MS agar plate.
Sterilisation4 degree in refrigerator for 2 days.
Protocol
Substrate Sterilising Procedureautoclave
Temperature22 °C average, 22 °C day, 22 °C night
Humidity80 % average, 80 % day, 80 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: None. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: 5 mM hydrogen peroxide was added into media from the beginning.
Additional Organism Information:
Sample DescriptionThe whole seedlings were collected in the green safe light (Green LED lamp, wavelength 520~540 nm) and frozened in LN.
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:0.648975
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.963857
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.110621
Spike_AFFX-r2-Bs-dap_5_signal80.943390
NoiseAvg:2.50,Std:0.08,Min:2.3,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal30.628906
#P15487
Spike_AFFX-r2-Bs-phe_M_signal42.350704
Corner-Avg:12675,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal139.133499
Spike_AFFX-r2-Ec-bioB_3_signal85.376732
Spike_AFFX-r2-Bs-lys_M_signal23.685751
Spike_AFFX-r2-P1-cre_3_signal4295.064941
Spike_AFFX-r2-Bs-lys_3-5-ratio1.320716
Spike_AFFX-r2-Bs-dap_M_signal212.850677
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.313933
Spike_AFFX-r2-Ec-bioB_avg-signal100.461060
Spike_AFFX-r2-Bs-thr_avg-signal120.238586
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal886.515869
Spike_AFFX-r2-Bs-phe_5_signal58.530632
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1476.640381
RawQ2.545656
Spike_AFFX-r2-Bs-lys_5_signal28.868595
Signal(A)3.399548
%A30.635687
Signal(All)137.121567
Corner+Avg:181,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal296.826111
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal48.221611
Spike_AFFX-r2-Ec-bioD_avg-signal1181.578125
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.895660
Spike_AFFX-r2-Bs-lys_avg-signal30.227182
Spike_AFFX-r2-P1-cre_avg-signal4375.594238
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.468654
Spike_AFFX-r2-Bs-thr_3_signal224.017761
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-signal49.700977
Spike_AFFX-r2-Bs-dap_3_signal360.574860
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.665667
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal308.408295
#M335
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal38.127205
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.962445
Spike_AFFX-r2-Bs-thr_M_signal106.069084
Signal(P)200.162613
Spike_AFFX-r2-Bs-phe_3-5-ratio0.823870
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8419,Count:9
Spike_AFFX-r2-P1-cre_5_signal4456.123535
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6988
Signal(M)12.144204
BackgroundAvg:61.63,Std:0.67,Min:59.6,Max:63.3
Spike_AFFX-r2-Ec-bioC_avg-signal302.617188
Spike_AFFX-r2-Bs-dap_avg-signal218.122971
Spike_AFFX-r2-Bs-dap_3-5-ratio4.454655
Spike_AFFX-r2-Ec-bioB_5_signal76.872955
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.648975
NF1.000000
HZ4
Tau0.015000

Slide: Cheng_576-4_7-days_H2O2_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Cheng_576-4_7-days_H2O2_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: Cheng_576-4_7-days_H2O2_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: col-0
Stock Code:
Growth Conditions:
Stratificationthe seeds were sterilised in 50% bleach containing 0.02% Tween-20 for 10 min, then washed 5 times with distilled water. The seeds were dried on filter paper and sprinkled onto 1/2 MS agar plate.
Sterilisation4 degree in refrigerator for 2 days.
Protocol
Substrate Sterilising Procedureautoclave
Temperature22 °C average, 22 °C day, 22 °C night
Humidity80 % average, 80 % day, 80 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: None. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: 5 mM hydrogen peroxide was added into media from the beginning.
Additional Organism Information:
Sample DescriptionThe whole seedlings were collected in the green safe light (Green LED lamp, wavelength 520~540 nm) and frozened in LN.
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:0.695214
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-ratio1.072578
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.880010
Spike_AFFX-r2-Bs-dap_5_signal34.339767
NoiseAvg:2.52,Std:0.07,Min:2.3,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal25.973557
#P15221
Spike_AFFX-r2-Bs-phe_M_signal39.875744
Corner-Avg:10709,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal103.547058
Spike_AFFX-r2-Ec-bioB_3_signal71.812134
Spike_AFFX-r2-Bs-lys_M_signal15.126139
Spike_AFFX-r2-P1-cre_3_signal3805.237061
Spike_AFFX-r2-Bs-lys_3-5-ratio1.877720
Spike_AFFX-r2-Bs-dap_M_signal220.059265
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.887530
Spike_AFFX-r2-Ec-bioB_avg-signal85.654320
Spike_AFFX-r2-Bs-thr_avg-signal109.917580
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal729.019043
Spike_AFFX-r2-Bs-phe_5_signal43.592937
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1185.983154
RawQ2.509203
Spike_AFFX-r2-Bs-lys_5_signal22.975996
Signal(A)3.649627
%A31.613327
Signal(All)137.674652
Corner+Avg:160,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal289.276672
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal52.744183
Spike_AFFX-r2-Ec-bioD_avg-signal957.501099
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.729507
Spike_AFFX-r2-Bs-lys_avg-signal27.081541
Spike_AFFX-r2-P1-cre_avg-signal3676.492432
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.657168
Spike_AFFX-r2-Bs-thr_3_signal230.840759
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-signal45.404285
Spike_AFFX-r2-Bs-dap_3_signal353.157043
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.626821
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal295.519775
#M378
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal43.142483
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.978874
Spike_AFFX-r2-Bs-thr_M_signal72.938423
Signal(P)204.272308
Spike_AFFX-r2-Bs-phe_3-5-ratio1.209925
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7165,Count:9
Spike_AFFX-r2-P1-cre_5_signal3547.747803
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7211
Signal(M)12.731547
BackgroundAvg:61.57,Std:0.48,Min:59.7,Max:62.8
Spike_AFFX-r2-Ec-bioC_avg-signal292.398224
Spike_AFFX-r2-Bs-dap_avg-signal202.518692
Spike_AFFX-r2-Bs-dap_3-5-ratio10.284201
Spike_AFFX-r2-Ec-bioB_5_signal81.603745
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.695214
NF1.000000
HZ4
Tau0.015000

Slide: Cheng_576-5_7-days_light_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 ("Cheng_576-5_7-days_light_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: Cheng_576-5_7-days_light_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: col-0
Stock Code:
Growth Conditions:
Stratificationthe seeds were sterilised in 50% bleach containing 0.02% Tween-20 for 10 min, then washed 5 times with distilled water. The seeds were dried on filter paper and sprinkled onto 1/2 MS agar plate.
Sterilisation4 degree in refrigerator for 2 days.
Protocol
Substrate Sterilising Procedureautoclave
Temperature22 °C average, 22 °C day, 22 °C night
Humidity80 % average, 80 % day, 80 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: None. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: 5 mM hydrogen peroxide was added into media from the beginning.
Additional Organism Information:
Sample DescriptionThe whole seedlings were collected in the green safe light (Green LED lamp, wavelength 520~540 nm) and frozened in LN.
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:0.332113
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-ratio1.230632
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.115560
Spike_AFFX-r2-Bs-dap_5_signal33.183552
NoiseAvg:3.04,Std:0.10,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_signal18.585531
#P15988
Spike_AFFX-r2-Bs-phe_M_signal35.296982
Corner-Avg:13425,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal78.987076
Spike_AFFX-r2-Ec-bioB_3_signal59.353874
Spike_AFFX-r2-Bs-lys_M_signal12.004230
Spike_AFFX-r2-P1-cre_3_signal3269.479736
Spike_AFFX-r2-Bs-lys_3-5-ratio1.451951
Spike_AFFX-r2-Bs-dap_M_signal150.748184
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.629722
Spike_AFFX-r2-Ec-bioB_avg-signal63.848804
Spike_AFFX-r2-Bs-thr_avg-signal45.163593
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal576.783508
Spike_AFFX-r2-Bs-phe_5_signal30.819181
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1032.038940
RawQ2.695548
Spike_AFFX-r2-Bs-lys_5_signal17.614109
Signal(A)2.459703
%A28.509426
Signal(All)137.399445
Corner+Avg:226,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal210.588028
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.166784
Spike_AFFX-r2-Ec-bioD_avg-signal804.411255
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.092064
Spike_AFFX-r2-Bs-lys_avg-signal18.397722
Spike_AFFX-r2-P1-cre_avg-signal2963.114258
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.398509
Spike_AFFX-r2-Bs-thr_3_signal67.460312
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal31.427650
Spike_AFFX-r2-Bs-dap_3_signal186.142273
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.789300
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal255.366150
#M319
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal25.574829
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.824651
Spike_AFFX-r2-Bs-thr_M_signal49.444942
Signal(P)194.835373
Spike_AFFX-r2-Bs-phe_3-5-ratio0.913937
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11273,Count:9
Spike_AFFX-r2-P1-cre_5_signal2656.748535
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6503
Signal(M)9.586100
BackgroundAvg:67.49,Std:0.93,Min:65.1,Max:70.4
Spike_AFFX-r2-Ec-bioC_avg-signal232.977081
Spike_AFFX-r2-Bs-dap_avg-signal123.358002
Spike_AFFX-r2-Bs-dap_3-5-ratio5.609474
Spike_AFFX-r2-Ec-bioB_5_signal53.205467
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.332113
NF1.000000
HZ4
Tau0.015000

Slide: Cheng_576-6_7-days_light_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 ("Cheng_576-6_7-days_light_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: Cheng_576-6_7-days_light_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: col-0
Stock Code:
Growth Conditions:
Stratificationthe seeds were sterilised in 50% bleach containing 0.02% Tween-20 for 10 min, then washed 5 times with distilled water. The seeds were dried on filter paper and sprinkled onto 1/2 MS agar plate.
Sterilisation4 degree in refrigerator for 2 days.
Protocol
Substrate Sterilising Procedureautoclave
Temperature22 °C average, 22 °C day, 22 °C night
Humidity80 % average, 80 % day, 80 % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting(Source: None. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
in vivo Treatment: 5 mM hydrogen peroxide was added into media from the beginning.
Additional Organism Information:
Sample DescriptionThe whole seedlings were collected in the green safe light (Green LED lamp, wavelength 520~540 nm) and frozened in LN.
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:0.619442
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-ratio1.059908
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.930449
Spike_AFFX-r2-Bs-dap_5_signal101.606682
NoiseAvg:2.96,Std:0.10,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_signal38.933464
#P15161
Spike_AFFX-r2-Bs-phe_M_signal49.795223
Corner-Avg:13012,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal121.698875
Spike_AFFX-r2-Ec-bioB_3_signal91.830925
Spike_AFFX-r2-Bs-lys_M_signal22.471375
Spike_AFFX-r2-P1-cre_3_signal4582.270996
Spike_AFFX-r2-Bs-lys_3-5-ratio1.153468
Spike_AFFX-r2-Bs-dap_M_signal287.944733
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.219858
Spike_AFFX-r2-Ec-bioB_avg-signal104.075020
Spike_AFFX-r2-Bs-thr_avg-signal106.012718
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal982.568604
Spike_AFFX-r2-Bs-phe_5_signal56.215038
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1745.448853
RawQ2.899379
Spike_AFFX-r2-Bs-lys_5_signal40.914104
Signal(A)4.236754
%A31.823761
Signal(All)145.510941
Corner+Avg:199,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal358.207214
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal68.296394
Spike_AFFX-r2-Ec-bioD_avg-signal1364.008789
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.466461
Spike_AFFX-r2-Bs-lys_avg-signal36.859528
Spike_AFFX-r2-P1-cre_avg-signal4452.772461
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.709776
Spike_AFFX-r2-Bs-thr_3_signal164.293671
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-signal58.102219
Spike_AFFX-r2-Bs-dap_3_signal343.469208
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.776414
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal389.802826
#M390
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal47.193096
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.918945
Spike_AFFX-r2-Bs-thr_M_signal114.811005
Signal(P)216.497101
Spike_AFFX-r2-Bs-phe_3-5-ratio1.214913
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9542,Count:9
Spike_AFFX-r2-P1-cre_5_signal4323.273438
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7259
Signal(M)15.480450
BackgroundAvg:72.39,Std:0.34,Min:71.5,Max:73.3
Spike_AFFX-r2-Ec-bioC_avg-signal374.005005
Spike_AFFX-r2-Bs-dap_avg-signal244.340210
Spike_AFFX-r2-Bs-dap_3-5-ratio3.380380
Spike_AFFX-r2-Ec-bioB_5_signal98.695259
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.619442
NF1.000000
HZ4
Tau0.015000


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