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Experiment: Analysis MYB26 targets by using Dex inducible line

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-635

MALE STERILITY 35 (MS35/ MYB26) is a R2R3-type MYB transcription factor (Steiner-Large et al., 2003). MYB26 is suggested to be a key regulator in the process of lignified secondary thickening in the anther endothecium which provides mechanical force for anther dehiscence (Dawson et al., 1999). This microarray experiment aims to identify genes controlled by MYB26 and thus establish the precise role MYB26 plays during anther development. Comparisons of gene expression will be carried out between functional complemented ms35 mutant line-MYB26promoter::MYB26gDNA-GRYFP and ms35 mutant at the time points 0h, 2h, 4h and 6h after Dex treatment to identify genes with altered expression due to the functional MYB26 released by the Dex induction. The Dex treated ms35 mutant was chosen to ensure that the changes of gene expression are not due to the Dex effect. Plants were grown in growth room at 22h of daylight (167 umol.m2.sec-1) at 24 C and 2h of night at 24 C. Flowering plants with 3-5 sterile siliques were sprayed with 25uM Dex; closed buds were collected from both lines at the time points 0h, 2h, 4h and 6h. RNA was extracted using RNeasy Mini Kit (Qiagen, USA) and digested with DNase to eliminate genomic DNA contamination.

About the Experimenter

Name:Dr Caiyun Yang
Head of Lab Name: Zoe Wilson
Lab:
Address:Plant and Crop Sciences Division, Plant Sciences Building, School of Biosciences, University of Nottingham
Sutton Bonington Campus, College Road, Sutton Bonington, Nottinghamshire, LE12 5RD, UNITED KINGDOM
Postcode: LE125RD
Country: United Kingdom
 
Telephone Number: 01159516383
Fax Number: 01159516334

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: timepoint
Number of Slides:16
 
Experimental Parameters:
parametertimepoint
Quality Control Measures Taken:
References:
Reference Steiner-Large et al., 2003
Reference Dawson et al., 1999
 
Other Information:

Slides in this Experiment

Hybridisation Set: Yang: Analysis MYB26 targets by using Dex inducible line

Slide: Yang_635-10_Dex _2h_buds_MYB26-ms35_Rep2_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 ("Yang_635-10_Dex _2h_buds_MYB26-ms35_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: Yang_635-10_Dex _2h_buds_MYB26-ms35_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: ms35 transformed with MYB26pro:MYB26 GRYFP
Stock Code:
Genetic Background: Ler
Growth Conditions:
ProtocolPlants were grown in growth rooms at 22h of daylight and 2h of night at 22 C; in 3x4 well tray with 2 plants per well
Soil ConstituentsCommercial soil: Levington M3 mixed with intercept(The Scotts Company, UK)
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
Medium
Lighting(Source: High pressure sodium and metal halide. Wavelength: White)0.366666666666667 hour days, 0.0333333333333333 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: X-rays induced mutation mutation in
Tissue: buds
in vivo Treatment: When plants flowering with 3-5 silique (5 weeks), 25uM Dex +0.02% Silwet was spayed onto infloroscences and covered with lid. All unopened flower buds from primary infloroscences of 5 plats were collected.
Additional Organism Information:
Sample DescriptionAll unopened flower buds from primary infloroscences of 5 plants were collected at 2 hours after Dex treatment.
Other Information:
Timecourse start procedurewhen Dex was applied to plants

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:1.18119
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-ratio1.201311
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.030166
Spike_AFFX-r2-Bs-dap_5_signal2.196963
NoiseAvg:2.63,Std:0.06,Min:2.5,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_signal7.684821
#P14026
Spike_AFFX-r2-Bs-phe_M_signal10.034852
Corner-Avg:11510,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal37.114460
Spike_AFFX-r2-Ec-bioB_3_signal36.570515
Spike_AFFX-r2-Bs-lys_M_signal8.292949
Spike_AFFX-r2-P1-cre_3_signal9870.998047
Spike_AFFX-r2-Bs-lys_3-5-ratio2.457966
Spike_AFFX-r2-Bs-dap_M_signal31.296816
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.347288
Spike_AFFX-r2-Ec-bioB_avg-signal36.394875
Spike_AFFX-r2-Bs-thr_avg-signal18.095352
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal2807.172363
Spike_AFFX-r2-Bs-phe_5_signal1.004488
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal3202.933594
RawQ2.590076
Spike_AFFX-r2-Bs-lys_5_signal7.011321
Signal(A)7.395787
%A36.514687
Signal(All)144.351120
Corner+Avg:186,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal671.984802
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal13.077250
Spike_AFFX-r2-Ec-bioD_avg-signal3005.052979
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P61.490574
Spike_AFFX-r2-Bs-lys_avg-signal10.845954
Spike_AFFX-r2-P1-cre_avg-signal9043.924805
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.994739
Spike_AFFX-r2-Bs-thr_3_signal33.408131
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-signal8.038863
Spike_AFFX-r2-Bs-dap_3_signal77.600006
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.140982
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal580.608765
#M455
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal17.233589
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.157380
Spike_AFFX-r2-Bs-thr_M_signal13.193105
Signal(P)229.516510
Spike_AFFX-r2-Bs-phe_3-5-ratio13.018819
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8886,Count:9
Spike_AFFX-r2-P1-cre_5_signal8216.851563
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8329
Signal(M)26.046553
BackgroundAvg:65.26,Std:1.39,Min:61.3,Max:67.3
Spike_AFFX-r2-Ec-bioC_avg-signal626.296753
Spike_AFFX-r2-Bs-dap_avg-signal37.031261
Spike_AFFX-r2-Bs-dap_3-5-ratio35.321484
Spike_AFFX-r2-Ec-bioB_5_signal35.499649
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.181190
NF1.000000
HZ4
Tau0.015000

Slide: Yang_635-9_Dex _0h_buds_MYB26-ms35_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 ("Yang_635-9_Dex _0h_buds_MYB26-ms35_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: Yang_635-9_Dex _0h_buds_MYB26-ms35_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: ms35 transformed with MYB26pro:MYB26 GRYFP
Stock Code:
Genetic Background: Ler
Growth Conditions:
ProtocolPlants were grown in growth rooms at 22h of daylight and 2h of night at 22 C; in 3x4 well tray with 2 plants per well
Soil ConstituentsCommercial soil: Levington M3 mixed with intercept(The Scotts Company, UK)
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
Medium
Lighting(Source: High pressure sodium and metal halide. Wavelength: White)0.366666666666667 hour days, 0.0333333333333333 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: X-rays induced mutation mutation in
Tissue: buds
Additional Organism Information:
Sample DescriptionAll unopened flower buds from primary infloroscences of 5 plants were collected before Dex treatment.
Other Information:
Timecourse start procedureJust before Dex was applied to plants

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:0.733125
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-ratio1.360759
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.681880
Spike_AFFX-r2-Bs-dap_5_signal19.497271
NoiseAvg:2.79,Std:0.08,Min:2.5,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal9.800717
#P14946
Spike_AFFX-r2-Bs-phe_M_signal10.991669
Corner-Avg:12615,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal26.590532
Spike_AFFX-r2-Ec-bioB_3_signal23.796030
Spike_AFFX-r2-Bs-lys_M_signal8.565920
Spike_AFFX-r2-P1-cre_3_signal7469.009277
Spike_AFFX-r2-Bs-lys_3-5-ratio2.749667
Spike_AFFX-r2-Bs-dap_M_signal48.843418
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.056689
Spike_AFFX-r2-Ec-bioB_avg-signal28.428085
Spike_AFFX-r2-Bs-thr_avg-signal23.038467
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1741.004639
Spike_AFFX-r2-Bs-phe_5_signal8.019381
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2043.178223
RawQ2.635576
Spike_AFFX-r2-Bs-lys_5_signal7.129423
Signal(A)5.487567
%A32.551514
Signal(All)141.546661
Corner+Avg:209,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal443.250061
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal9.538258
Spike_AFFX-r2-Ec-bioD_avg-signal1892.091431
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P65.523895
Spike_AFFX-r2-Bs-lys_avg-signal11.766294
Spike_AFFX-r2-P1-cre_avg-signal6478.933105
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.924595
Spike_AFFX-r2-Bs-thr_3_signal39.758465
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-signal9.516436
Spike_AFFX-r2-Bs-dap_3_signal96.459106
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.173563
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal406.887909
#M439
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal19.603540
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.089367
Spike_AFFX-r2-Bs-thr_M_signal19.556219
Signal(P)212.718750
Spike_AFFX-r2-Bs-phe_3-5-ratio1.189401
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10252,Count:9
Spike_AFFX-r2-P1-cre_5_signal5488.856934
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7425
Signal(M)19.680450
BackgroundAvg:64.28,Std:0.73,Min:62.1,Max:66.4
Spike_AFFX-r2-Ec-bioC_avg-signal425.068970
Spike_AFFX-r2-Bs-dap_avg-signal54.933262
Spike_AFFX-r2-Bs-dap_3-5-ratio4.947313
Spike_AFFX-r2-Ec-bioB_5_signal34.897694
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.733125
NF1.000000
HZ4
Tau0.015000

Slide: Yang_635-7_Dex_4h_buds_ms35 mutant_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 ("Yang_635-7_Dex_4h_buds_ms35 mutant_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: Yang_635-7_Dex_4h_buds_ms35 mutant_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: ms35 mutant
Stock Code:
Genetic Background: Ler
Growth Conditions:
ProtocolPlants were grown in growth rooms at 22h of daylight and 2h of night at 22 C; in 3x4 well tray with 2 plants per well
Soil ConstituentsCommercial soil: Levington M3 mixed with intercept(The Scotts Company, UK)
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
Medium
Lighting(Source: High pressure sodium and metal halide. Wavelength: White)0.366666666666667 hour days, 0.0333333333333333 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: X-rays induced mutation mutation in
Tissue: buds
in vivo Treatment: When plants flowering with 3-5 silique (5 weeks), 25uM Dex +0.02% Silwet was spayed onto infloroscences and covered with lid. All unopened flower buds from primary infloroscences of 5 plats were collected.
Additional Organism Information:
Sample DescriptionAll unopened flower buds from primary infloroscences of 5 plants were collected 4 hours after Dex treatment.
Other Information:
Timecourse start procedureWhen Dex was applied to plants

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:0.740818
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-ratio1.213203
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.071715
Spike_AFFX-r2-Bs-dap_5_signal13.671503
NoiseAvg:2.83,Std:0.08,Min:2.7,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_signal3.286724
#P14907
Spike_AFFX-r2-Bs-phe_M_signal9.950018
Corner-Avg:11145,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal17.452166
Spike_AFFX-r2-Ec-bioB_3_signal19.409374
Spike_AFFX-r2-Bs-lys_M_signal3.717165
Spike_AFFX-r2-P1-cre_3_signal5312.056641
Spike_AFFX-r2-Bs-lys_3-5-ratio3.955578
Spike_AFFX-r2-Bs-dap_M_signal44.172539
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.138288
Spike_AFFX-r2-Ec-bioB_avg-signal18.324041
Spike_AFFX-r2-Bs-thr_avg-signal19.933741
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1023.036804
Spike_AFFX-r2-Bs-phe_5_signal8.644130
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1471.900757
RawQ2.618236
Spike_AFFX-r2-Bs-lys_5_signal6.312573
Signal(A)5.376043
%A32.770714
Signal(All)140.788040
Corner+Avg:191,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal259.574127
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal13.952043
Spike_AFFX-r2-Ec-bioD_avg-signal1247.468750
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P65.352913
Spike_AFFX-r2-Bs-lys_avg-signal11.666537
Spike_AFFX-r2-P1-cre_avg-signal4845.297852
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.876370
Spike_AFFX-r2-Bs-thr_3_signal36.608482
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-signal10.848731
Spike_AFFX-r2-Bs-dap_3_signal87.764229
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.438756
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal214.906570
#M428
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.969872
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.207846
Spike_AFFX-r2-Bs-thr_M_signal19.906015
Signal(P)212.174850
Spike_AFFX-r2-Bs-phe_3-5-ratio1.614048
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9269,Count:9
Spike_AFFX-r2-P1-cre_5_signal4378.539063
Spike_AFFX-r2-Bs-phe_M_detectionM
#A7475
Signal(M)19.389769
BackgroundAvg:62.15,Std:0.42,Min:61.1,Max:63.3
Spike_AFFX-r2-Ec-bioC_avg-signal237.240356
Spike_AFFX-r2-Bs-dap_avg-signal48.536091
Spike_AFFX-r2-Bs-dap_3-5-ratio6.419501
Spike_AFFX-r2-Ec-bioB_5_signal18.110580
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.740818
NF1.000000
HZ4
Tau0.015000

Slide: Yang_635-6_Dex_2h_buds_ms35 mutant_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 ("Yang_635-6_Dex_2h_buds_ms35 mutant_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: Yang_635-6_Dex_2h_buds_ms35 mutant_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: ms35 mutant
Stock Code:
Genetic Background: Ler
Growth Conditions:
ProtocolPlants were grown in growth rooms at 22h of daylight and 2h of night at 22 C; in 3x4 well tray with 2 plants per well
Soil ConstituentsCommercial soil: Levington M3 mixed with intercept(The Scotts Company, UK)
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
Medium
Lighting(Source: High pressure sodium and metal halide. Wavelength: White)0.366666666666667 hour days, 0.0333333333333333 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: X-rays induced mutation mutation in
Tissue: buds
in vivo Treatment: When plants flowering with 3-5 silique (5 weeks), 25uM Dex +0.02% Silwet was spayed onto infloroscences and covered with lid. All unopened flower buds from primary infloroscences of 5 plats were collected.
Additional Organism Information:
Sample DescriptionAll unopened flower buds from primary infloroscences of 5 plants were collected before Dex treatment.
Other Information:
Timecourse start procedureWhen Dex was applied to plants

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:0.581477
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-ratio1.309137
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.628238
Spike_AFFX-r2-Bs-dap_5_signal19.703615
NoiseAvg:2.75,Std:0.05,Min:2.6,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_signal0.742199
#P15293
Spike_AFFX-r2-Bs-phe_M_signal7.629135
Corner-Avg:11128,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal12.846308
Spike_AFFX-r2-Ec-bioB_3_signal11.400446
Spike_AFFX-r2-Bs-lys_M_signal9.140505
Spike_AFFX-r2-P1-cre_3_signal5131.029785
Spike_AFFX-r2-Bs-lys_3-5-ratio2.361608
Spike_AFFX-r2-Bs-dap_M_signal34.288895
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio26.397984
Spike_AFFX-r2-Ec-bioB_avg-signal14.131149
Spike_AFFX-r2-Bs-thr_avg-signal14.162833
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal956.493774
Spike_AFFX-r2-Bs-phe_5_signal7.030515
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1270.583984
RawQ2.562448
Spike_AFFX-r2-Bs-lys_5_signal6.228603
Signal(A)4.137094
%A31.144236
Signal(All)138.879593
Corner+Avg:197,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal249.095718
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal11.724558
Spike_AFFX-r2-Ec-bioD_avg-signal1113.538818
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P67.045158
Spike_AFFX-r2-Bs-lys_avg-signal10.026208
Spike_AFFX-r2-P1-cre_avg-signal4525.214844
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.810609
Spike_AFFX-r2-Bs-thr_3_signal26.397984
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-signal8.794736
Spike_AFFX-r2-Bs-dap_3_signal94.087250
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.328377
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal217.394424
#M413
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal14.709516
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.145824
Spike_AFFX-r2-Bs-thr_M_signal15.348317
Signal(P)204.815247
Spike_AFFX-r2-Bs-phe_3-5-ratio1.667667
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9717,Count:9
Spike_AFFX-r2-P1-cre_5_signal3919.399902
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7104
Signal(M)15.046519
BackgroundAvg:58.75,Std:0.27,Min:58.1,Max:59.7
Spike_AFFX-r2-Ec-bioC_avg-signal233.245071
Spike_AFFX-r2-Bs-dap_avg-signal49.359921
Spike_AFFX-r2-Bs-dap_3-5-ratio4.775126
Spike_AFFX-r2-Ec-bioB_5_signal18.146694
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.581477
NF1.000000
HZ4
Tau0.015000

Slide: Yang_635-5_Dex_0h_buds_ms35 mutant_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 ("Yang_635-5_Dex_0h_buds_ms35 mutant_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: Yang_635-5_Dex_0h_buds_ms35 mutant_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: ms35 mutant
Stock Code:
Genetic Background: Ler
Growth Conditions:
ProtocolPlants were grown in growth rooms at 22h of daylight and 2h of night at 22 C; in 3x4 well tray with 2 plants per well
Soil ConstituentsCommercial soil: Levington M3 mixed with intercept(The Scotts Company, UK)
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
Medium
Lighting(Source: High pressure sodium and metal halide. Wavelength: White)0.366666666666667 hour days, 0.0333333333333333 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: X-rays induced mutation mutation in
Tissue: buds
Additional Organism Information:
Sample DescriptionAll unopened flower buds from primary infloroscences of 5 plants were collected before Dex treatment.
Other Information:
Timecourse start procedureJust before Dex was applied to plants

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:0.673018
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-ratio1.240671
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.736416
Spike_AFFX-r2-Bs-dap_5_signal23.141132
NoiseAvg:2.83,Std:0.07,Min:2.6,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal0.380848
#P15146
Spike_AFFX-r2-Bs-phe_M_signal6.719971
Corner-Avg:12212,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal21.781279
Spike_AFFX-r2-Ec-bioB_3_signal19.215481
Spike_AFFX-r2-Bs-lys_M_signal12.618356
Spike_AFFX-r2-P1-cre_3_signal6851.041992
Spike_AFFX-r2-Bs-lys_3-5-ratio1.547047
Spike_AFFX-r2-Bs-dap_M_signal53.876827
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio35.527599
Spike_AFFX-r2-Ec-bioB_avg-signal22.363327
Spike_AFFX-r2-Bs-thr_avg-signal19.094921
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1583.032959
Spike_AFFX-r2-Bs-phe_5_signal8.265998
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1763.441650
RawQ2.599000
Spike_AFFX-r2-Bs-lys_5_signal8.029374
Signal(A)4.363769
%A31.705393
Signal(All)144.118378
Corner+Avg:215,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal337.913940
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal18.064774
Spike_AFFX-r2-Ec-bioD_avg-signal1673.237305
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.400703
Spike_AFFX-r2-Bs-lys_avg-signal11.023183
Spike_AFFX-r2-P1-cre_avg-signal6186.544922
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.893906
Spike_AFFX-r2-Bs-thr_3_signal35.527599
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-signal11.016914
Spike_AFFX-r2-Bs-dap_3_signal116.318512
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.113964
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal302.481476
#M432
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal12.421820
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.117139
Spike_AFFX-r2-Bs-thr_M_signal21.376318
Signal(P)214.476547
Spike_AFFX-r2-Bs-phe_3-5-ratio2.185432
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9929,Count:9
Spike_AFFX-r2-P1-cre_5_signal5522.047852
Spike_AFFX-r2-Bs-phe_M_detectionM
#A7232
Signal(M)16.943998
BackgroundAvg:63.11,Std:0.51,Min:62.1,Max:64.5
Spike_AFFX-r2-Ec-bioC_avg-signal320.197693
Spike_AFFX-r2-Bs-dap_avg-signal64.445488
Spike_AFFX-r2-Bs-dap_3-5-ratio5.026483
Spike_AFFX-r2-Ec-bioB_5_signal26.093225
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.673018
NF1.000000
HZ4
Tau0.015000

Slide: Yang_635-4_Dex _6h_buds_MYB26-ms35_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 ("Yang_635-4_Dex _6h_buds_MYB26-ms35_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: Yang_635-4_Dex _6h_buds_MYB26-ms35_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: ms35 transformed with MYB26pro:MYB26 GRYFP
Stock Code:
Genetic Background: Ler
Growth Conditions:
ProtocolPlants were grown in growth rooms at 22h of daylight and 2h of night at 22 C; in 3x4 well tray with 2 plants per well
Soil ConstituentsCommercial soil: Levington M3 mixed with intercept(The Scotts Company, UK)
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
Medium
Lighting(Source: High pressure sodium and metal halide. Wavelength: White)0.366666666666667 hour days, 0.0333333333333333 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: X-rays induced mutation mutation in
Tissue: buds
in vivo Treatment: When plants flowering with 3-5 silique (5 weeks), 25uM Dex +0.02% Silwet was spayed onto infloroscences and covered with lid. All unopened flower buds from primary infloroscences of 5 plats were collected.
Additional Organism Information:
Sample DescriptionAll unopened flower buds from primary infloroscences of 5 plants were collected at 6 hours after Dex treatment.
Other Information:
Timecourse start procedurewhen Dex was applied to plants

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:0.725185
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-ratio1.289985
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.567971
Spike_AFFX-r2-Bs-dap_5_signal25.433855
NoiseAvg:2.62,Std:0.07,Min:2.5,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_signal7.190703
#P15157
Spike_AFFX-r2-Bs-phe_M_signal11.575464
Corner-Avg:11721,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal16.145685
Spike_AFFX-r2-Ec-bioB_3_signal14.439093
Spike_AFFX-r2-Bs-lys_M_signal12.309411
Spike_AFFX-r2-P1-cre_3_signal6591.873535
Spike_AFFX-r2-Bs-lys_3-5-ratio1.329037
Spike_AFFX-r2-Bs-dap_M_signal58.336052
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.946794
Spike_AFFX-r2-Ec-bioB_avg-signal18.669004
Spike_AFFX-r2-Bs-thr_avg-signal20.786825
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1353.562622
Spike_AFFX-r2-Bs-phe_5_signal9.714501
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1676.859253
RawQ2.407829
Spike_AFFX-r2-Bs-lys_5_signal8.369950
Signal(A)4.536398
%A31.871986
Signal(All)141.318558
Corner+Avg:199,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal297.794250
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal8.592961
Spike_AFFX-r2-Ec-bioD_avg-signal1515.210938
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P66.448929
Spike_AFFX-r2-Bs-lys_avg-signal10.601111
Spike_AFFX-r2-P1-cre_avg-signal5850.956055
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.679088
Spike_AFFX-r2-Bs-thr_3_signal35.570923
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-signal9.960976
Spike_AFFX-r2-Bs-dap_3_signal107.282135
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.238849
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal282.948700
#M383
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal11.123973
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.052467
Spike_AFFX-r2-Bs-thr_M_signal19.598848
Signal(P)210.068649
Spike_AFFX-r2-Bs-phe_3-5-ratio0.884550
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10030,Count:9
Spike_AFFX-r2-P1-cre_5_signal5110.038574
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7270
Signal(M)16.935637
BackgroundAvg:59.14,Std:0.45,Min:58.0,Max:60.1
Spike_AFFX-r2-Ec-bioC_avg-signal290.371460
Spike_AFFX-r2-Bs-dap_avg-signal63.684017
Spike_AFFX-r2-Bs-dap_3-5-ratio4.218084
Spike_AFFX-r2-Ec-bioB_5_signal25.422232
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.725185
NF1.000000
HZ4
Tau0.015000

Slide: Yang_635-3_Dex _4h_buds_MYB26-ms35_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 ("Yang_635-3_Dex _4h_buds_MYB26-ms35_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: Yang_635-3_Dex _4h_buds_MYB26-ms35_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: ms35 transformed with MYB26pro:MYB26 GRYFP
Stock Code:
Genetic Background: Ler
Growth Conditions:
ProtocolPlants were grown in growth rooms at 22h of daylight and 2h of night at 22 C; in 3x4 well tray with 2 plants per well
Soil ConstituentsCommercial soil: Levington M3 mixed with intercept(The Scotts Company, UK)
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
Medium
Lighting(Source: High pressure sodium and metal halide. Wavelength: White)0.366666666666667 hour days, 0.0333333333333333 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: X-rays induced mutation mutation in
Tissue: buds
in vivo Treatment: When plants flowering with 3-5 silique (5 weeks), 25uM Dex +0.02% Silwet was spayed onto infloroscences and covered with lid. All unopened flower buds from primary infloroscences of 5 plats were collected.
Additional Organism Information:
Sample DescriptionAll unopened flower buds from primary infloroscences of 5 plants were collected at 4 hours after Dex treatment.
Other Information:
Timecourse start procedurewhen Dex was applied to plants

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:0.724907
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-ratio1.269215
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.955746
Spike_AFFX-r2-Bs-dap_5_signal23.450626
NoiseAvg:2.63,Std:0.06,Min:2.5,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal2.382503
#P15221
Spike_AFFX-r2-Bs-phe_M_signal15.378775
Corner-Avg:9883,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal16.026712
Spike_AFFX-r2-Ec-bioB_3_signal14.734043
Spike_AFFX-r2-Bs-lys_M_signal9.850821
Spike_AFFX-r2-P1-cre_3_signal5475.668457
Spike_AFFX-r2-Bs-lys_3-5-ratio4.854762
Spike_AFFX-r2-Bs-dap_M_signal64.458260
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio18.249136
Spike_AFFX-r2-Ec-bioB_avg-signal15.392345
Spike_AFFX-r2-Bs-thr_avg-signal22.841475
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1042.308105
Spike_AFFX-r2-Bs-phe_5_signal10.605062
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1422.199829
RawQ2.468975
Spike_AFFX-r2-Bs-lys_5_signal3.428208
Signal(A)4.744632
%A31.512495
Signal(All)139.355225
Corner+Avg:167,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal264.949890
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal20.241194
Spike_AFFX-r2-Ec-bioD_avg-signal1232.253906
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionM
%P66.729507
Spike_AFFX-r2-Bs-lys_avg-signal9.974053
Spike_AFFX-r2-P1-cre_avg-signal4894.943359
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.758001
Spike_AFFX-r2-Bs-thr_3_signal43.478615
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-signal15.408343
Spike_AFFX-r2-Bs-dap_3_signal124.111420
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.364472
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal276.010193
#M401
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal16.643133
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.959928
Spike_AFFX-r2-Bs-thr_M_signal22.663305
Signal(P)206.145477
Spike_AFFX-r2-Bs-phe_3-5-ratio1.908635
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8115,Count:9
Spike_AFFX-r2-P1-cre_5_signal4314.218262
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7188
Signal(M)17.077610
BackgroundAvg:61.01,Std:0.58,Min:59.4,Max:62.7
Spike_AFFX-r2-Ec-bioC_avg-signal270.480042
Spike_AFFX-r2-Bs-dap_avg-signal70.673431
Spike_AFFX-r2-Bs-dap_3-5-ratio5.292457
Spike_AFFX-r2-Ec-bioB_5_signal15.416282
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.724907
NF1.000000
HZ4
Tau0.015000

Slide: Yang_635-1_Dex _0h_buds_MYB26-ms35_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 ("Yang_635-1_Dex _0h_buds_MYB26-ms35_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: Yang_635-1_Dex _0h_buds_MYB26-ms35_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: ms35 transformed with MYB26pro:MYB26GRYFP
Stock Code:
Genetic Background: Ler
Growth Conditions:
ProtocolPlants were grown in growth rooms at 22h of daylight and 2h of night at 22 C; in 3x4 well tray with 2 plants per well
Soil ConstituentsLevington M3 mixed with intercept(The Scotts Company, UK)
Temperature22 C °C average, 22 C °C day, 22 C °C night
Humidity50% % average, 50% % day, 50% % night
Medium
Lighting(Source: High pressure sodium and metal halide. Wavelength: White)0.366666666666667 hour days, 0.0333333333333333 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Genetic Variation: X-rays induced mutation mutation in
Tissue: buds
Additional Organism Information:
Sample DescriptionWhen plants flowering with 3-5 silique (5 weeks), all unopened flower buds were collected
Other Information:
Timecourse start procedureJust before the Dex treatment

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:0.700185
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-ratio1.302289
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.818874
Spike_AFFX-r2-Bs-dap_5_signal27.129950
NoiseAvg:2.72,Std:0.15,Min:2.5,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_signal0.449734
#P15205
Spike_AFFX-r2-Bs-phe_M_signal13.472029
Corner-Avg:12209,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal19.937435
Spike_AFFX-r2-Ec-bioB_3_signal19.702589
Spike_AFFX-r2-Bs-lys_M_signal11.731483
Spike_AFFX-r2-P1-cre_3_signal6242.214844
Spike_AFFX-r2-Bs-lys_3-5-ratio1.783529
Spike_AFFX-r2-Bs-dap_M_signal59.214897
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio31.633453
Spike_AFFX-r2-Ec-bioB_avg-signal21.233534
Spike_AFFX-r2-Bs-thr_avg-signal15.381265
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1358.278809
Spike_AFFX-r2-Bs-phe_5_signal10.034733
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1637.278198
RawQ2.390970
Spike_AFFX-r2-Bs-lys_5_signal9.789533
Signal(A)4.876554
%A31.635248
Signal(All)141.230499
Corner+Avg:208,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal268.837891
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal17.352039
Spike_AFFX-r2-Ec-bioD_avg-signal1497.778564
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P66.659363
Spike_AFFX-r2-Bs-lys_avg-signal12.993645
Spike_AFFX-r2-P1-cre_avg-signal5517.740234
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_signal31.633453
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-signal13.619601
Spike_AFFX-r2-Bs-dap_3_signal114.078316
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.205407
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal267.453369
#M389
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal17.459919
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.005177
Spike_AFFX-r2-Bs-thr_M_signal14.060607
Signal(P)209.128891
Spike_AFFX-r2-Bs-phe_3-5-ratio1.729198
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9325,Count:9
Spike_AFFX-r2-P1-cre_5_signal4793.265137
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7216
Signal(M)16.642187
BackgroundAvg:54.06,Std:2.49,Min:50.4,Max:62.6
Spike_AFFX-r2-Ec-bioC_avg-signal268.145630
Spike_AFFX-r2-Bs-dap_avg-signal66.807716
Spike_AFFX-r2-Bs-dap_3-5-ratio4.204885
Spike_AFFX-r2-Ec-bioB_5_signal24.060579
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.700185
NF1.000000
HZ4
Tau0.015000

Slide: Yang_635-2_Dex _2h_buds_MYB26-ms35_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 ("Yang_635-2_Dex _2h_buds_MYB26-ms35_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: Yang_635-2_Dex _2h_buds_MYB26-ms35_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: ms35 transformed with MYB26pro:MYB26 GRYFP
Stock Code:
Genetic Background: Ler
Growth Conditions:
ProtocolPlants were grown in growth rooms at 22h of daylight and 2h of night at 22 C; in 3x4 well tray with 2 plants per well
Soil ConstituentsCommercial soil: Levington M3 mixed with intercept(The Scotts Company, UK)
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
Medium
Lighting(Source: High pressure sodium and metal halide. Wavelength: White)0.366666666666667 hour days, 0.0333333333333333 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: X-rays induced mutation mutation in
Tissue: buds
in vivo Treatment: When plants flowering with 3-5 silique (5 weeks), 25uM Dex +0.02% Silwet was spayed onto infloroscences and covered with lid. All unopened flower buds from primary infloroscences of 5 plats were collected.
Additional Organism Information:
Sample DescriptionAll unopened flower buds from primary infloroscences of 5 plants were collected at 2 hours after Dex treatment.
Other Information:
Timecourse start procedurewhen Dex was applied to plants

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:0.813875
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-ratio1.365643
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.647504
Spike_AFFX-r2-Bs-dap_5_signal32.484650
NoiseAvg:2.52,Std:0.07,Min:2.4,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.491014
#P15103
Spike_AFFX-r2-Bs-phe_M_signal6.940510
Corner-Avg:11299,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal29.754379
Spike_AFFX-r2-Ec-bioB_3_signal17.227915
Spike_AFFX-r2-Bs-lys_M_signal12.365110
Spike_AFFX-r2-P1-cre_3_signal7765.433594
Spike_AFFX-r2-Bs-lys_3-5-ratio3.267797
Spike_AFFX-r2-Bs-dap_M_signal71.872643
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.440041
Spike_AFFX-r2-Ec-bioB_avg-signal24.529646
Spike_AFFX-r2-Bs-thr_avg-signal26.334162
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1577.815308
Spike_AFFX-r2-Bs-phe_5_signal12.373387
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1876.781006
RawQ2.403615
Spike_AFFX-r2-Bs-lys_5_signal5.658216
Signal(A)5.130651
%A31.841297
Signal(All)141.359619
Corner+Avg:204,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal391.052277
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.220579
Spike_AFFX-r2-Ec-bioD_avg-signal1727.298096
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P66.212189
Spike_AFFX-r2-Bs-lys_avg-signal12.171077
Spike_AFFX-r2-P1-cre_avg-signal6725.859375
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.946515
Spike_AFFX-r2-Bs-thr_3_signal42.969601
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-signal13.511493
Spike_AFFX-r2-Bs-dap_3_signal124.608482
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.189481
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal343.286499
#M444
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal18.489904
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.139143
Spike_AFFX-r2-Bs-thr_M_signal23.541872
Signal(P)210.488068
Spike_AFFX-r2-Bs-phe_3-5-ratio1.715018
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9405,Count:9
Spike_AFFX-r2-P1-cre_5_signal5686.284668
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7263
Signal(M)18.350834
BackgroundAvg:57.21,Std:0.45,Min:55.8,Max:59.0
Spike_AFFX-r2-Ec-bioC_avg-signal367.169373
Spike_AFFX-r2-Bs-dap_avg-signal76.321922
Spike_AFFX-r2-Bs-dap_3-5-ratio3.835919
Spike_AFFX-r2-Ec-bioB_5_signal26.606646
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.813875
NF1.000000
HZ4
Tau0.015000

Slide: Yang_635-8_Dex_6h_buds_ms35 mutant_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 ("Yang_635-8_Dex_6h_buds_ms35 mutant_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: Yang_635-8_Dex_6h_buds_ms35 mutant_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: ms35 mutant
Stock Code:
Genetic Background: Ler
Growth Conditions:
ProtocolPlants were grown in growth rooms at 22h of daylight and 2h of night at 22 C; in 3x4 well tray with 2 plants per well
Soil ConstituentsCommercial soil: Levington M3 mixed with intercept(The Scotts Company, UK)
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
Medium
Lighting(Source: High pressure sodium and metal halide. Wavelength: White)0.366666666666667 hour days, 0.0333333333333333 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: X-rays induced mutation mutation in
Tissue: buds
in vivo Treatment: When plants flowering with 3-5 silique (5 weeks), 25uM Dex +0.02% Silwet was spayed onto infloroscences and covered with lid. All unopened flower buds from primary infloroscences of 5 plats were collected.
Additional Organism Information:
Sample DescriptionAll unopened flower buds from primary infloroscences of 5 plants were collected 6 hours after Dex treatment.
Other Information:
Timecourse start procedureWhen Dex was applied to plants

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:0.76488
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-ratio1.223870
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.008740
Spike_AFFX-r2-Bs-dap_5_signal17.340488
NoiseAvg:2.53,Std:0.05,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_signal2.816565
#P14985
Spike_AFFX-r2-Bs-phe_M_signal15.404770
Corner-Avg:11389,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal25.106482
Spike_AFFX-r2-Ec-bioB_3_signal23.746546
Spike_AFFX-r2-Bs-lys_M_signal12.677206
Spike_AFFX-r2-P1-cre_3_signal7029.612793
Spike_AFFX-r2-Bs-lys_3-5-ratio1.881295
Spike_AFFX-r2-Bs-dap_M_signal44.915394
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio12.087711
Spike_AFFX-r2-Ec-bioB_avg-signal24.131273
Spike_AFFX-r2-Bs-thr_avg-signal17.574789
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1664.780151
Spike_AFFX-r2-Bs-phe_5_signal11.875614
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2101.949463
RawQ2.268653
Spike_AFFX-r2-Bs-lys_5_signal8.139359
Signal(A)4.883136
%A32.472599
Signal(All)144.242798
Corner+Avg:190,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal342.428497
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal11.433313
Spike_AFFX-r2-Ec-bioD_avg-signal1883.364746
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P65.694870
Spike_AFFX-r2-Bs-lys_avg-signal12.043033
Spike_AFFX-r2-P1-cre_avg-signal6386.684570
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.832530
Spike_AFFX-r2-Bs-thr_3_signal34.045822
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-signal12.904567
Spike_AFFX-r2-Bs-dap_3_signal101.017097
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.262599
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal317.619934
#M418
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal15.312533
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.078108
Spike_AFFX-r2-Bs-thr_M_signal15.861981
Signal(P)216.671432
Spike_AFFX-r2-Bs-phe_3-5-ratio0.962756
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10410,Count:9
Spike_AFFX-r2-P1-cre_5_signal5743.756836
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7407
Signal(M)17.194706
BackgroundAvg:55.85,Std:0.54,Min:54.5,Max:57.2
Spike_AFFX-r2-Ec-bioC_avg-signal330.024231
Spike_AFFX-r2-Bs-dap_avg-signal54.424328
Spike_AFFX-r2-Bs-dap_3-5-ratio5.825505
Spike_AFFX-r2-Ec-bioB_5_signal23.540794
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.764880
NF1.000000
HZ4
Tau0.015000

Slide: Yang_635-11_Dex _4h_buds_MYB26-ms35_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 ("Yang_635-11_Dex _4h_buds_MYB26-ms35_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: Yang_635-11_Dex _4h_buds_MYB26-ms35_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: ms35 transformed with MYB26pro:MYB26 GRYFP
Stock Code:
Genetic Background: Ler
Growth Conditions:
ProtocolPlants were grown in growth rooms at 22h of daylight and 2h of night at 22 C; in 3x4 well tray with 2 plants per well
Soil ConstituentsCommercial soil: Levington M3 mixed with intercept(The Scotts Company, UK)
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
Medium
Lighting(Source: High pressure sodium and metal halide. Wavelength: White)0.366666666666667 hour days, 0.0333333333333333 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: X-rays induced mutation mutation in
Tissue: buds
in vivo Treatment: When plants flowering with 3-5 silique (5 weeks), 25uM Dex +0.02% Silwet was spayed onto infloroscences and covered with lid. All unopened flower buds from primary infloroscences of 5 plats were collected.
Additional Organism Information:
Sample DescriptionAll unopened flower buds from primary infloroscences of 5 plants were collected at 4 hours after Dex treatment.
Other Information:
Timecourse start procedurewhen Dex was applied to plants

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:0.686184
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-ratio1.129285
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.897503
Spike_AFFX-r2-Bs-dap_5_signal12.831371
NoiseAvg:2.76,Std:0.08,Min:2.6,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_signal3.892540
#P15278
Spike_AFFX-r2-Bs-phe_M_signal11.396030
Corner-Avg:10533,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal10.912585
Spike_AFFX-r2-Ec-bioB_3_signal10.396624
Spike_AFFX-r2-Bs-lys_M_signal16.296000
Spike_AFFX-r2-P1-cre_3_signal4928.894531
Spike_AFFX-r2-Bs-lys_3-5-ratio3.252505
Spike_AFFX-r2-Bs-dap_M_signal42.734501
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.930547
Spike_AFFX-r2-Ec-bioB_avg-signal10.964382
Spike_AFFX-r2-Bs-thr_avg-signal20.131880
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1177.737061
Spike_AFFX-r2-Bs-phe_5_signal5.652167
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1539.002197
RawQ2.534698
Spike_AFFX-r2-Bs-lys_5_signal6.800611
Signal(A)4.613583
%A31.297676
Signal(All)137.678970
Corner+Avg:174,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal284.888855
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.166731
Spike_AFFX-r2-Ec-bioD_avg-signal1358.369629
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P66.979393
Spike_AFFX-r2-Bs-lys_avg-signal15.071877
Spike_AFFX-r2-P1-cre_avg-signal4646.753906
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.722929
Spike_AFFX-r2-Bs-thr_3_signal38.655048
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-signal13.071643
Spike_AFFX-r2-Bs-dap_3_signal106.766808
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.306745
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal258.977539
#M393
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal22.119020
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.100052
Spike_AFFX-r2-Bs-thr_M_signal17.848047
Signal(P)202.966721
Spike_AFFX-r2-Bs-phe_3-5-ratio3.921811
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8681,Count:9
Spike_AFFX-r2-P1-cre_5_signal4364.613281
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7139
Signal(M)16.782480
BackgroundAvg:61.97,Std:1.42,Min:58.7,Max:64.7
Spike_AFFX-r2-Ec-bioC_avg-signal271.933197
Spike_AFFX-r2-Bs-dap_avg-signal54.110897
Spike_AFFX-r2-Bs-dap_3-5-ratio8.320764
Spike_AFFX-r2-Ec-bioB_5_signal11.583938
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.686184
NF1.000000
HZ4
Tau0.015000

Slide: Yang_635-16_Dex_6h_buds_ms35 mutant_Rep2_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 ("Yang_635-16_Dex_6h_buds_ms35 mutant_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: Yang_635-16_Dex_6h_buds_ms35 mutant_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: ms35 mutant
Stock Code:
Genetic Background: Ler
Growth Conditions:
ProtocolPlants were grown in growth rooms at 22h of daylight and 2h of night at 22 C; in 3x4 well tray with 2 plants per well
Soil ConstituentsCommercial soil: Levington M3 mixed with intercept(The Scotts Company, UK)
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
Medium
Lighting(Source: High pressure sodium and metal halide. Wavelength: White)0.366666666666667 hour days, 0.0333333333333333 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: X-rays induced mutation mutation in
Tissue: buds
in vivo Treatment: When plants flowering with 3-5 silique (5 weeks), 25uM Dex +0.02% Silwet was spayed onto infloroscences and covered with lid. All unopened flower buds from primary infloroscences of 5 plats were collected.
Additional Organism Information:
Sample DescriptionAll unopened flower buds from primary infloroscences of 5 plants were collected 6 hours after Dex treatment.
Other Information:
Timecourse start procedureWhen Dex was applied to plants

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:0.823572
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-ratio1.146428
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.750586
Spike_AFFX-r2-Bs-dap_5_signal14.862983
NoiseAvg:2.75,Std:0.11,Min:2.5,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.675099
#P14661
Spike_AFFX-r2-Bs-phe_M_signal6.470697
Corner-Avg:9795,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal22.041302
Spike_AFFX-r2-Ec-bioB_3_signal19.843359
Spike_AFFX-r2-Bs-lys_M_signal2.165800
Spike_AFFX-r2-P1-cre_3_signal5772.898926
Spike_AFFX-r2-Bs-lys_3-5-ratio4.976069
Spike_AFFX-r2-Bs-dap_M_signal37.232090
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.011111
Spike_AFFX-r2-Ec-bioB_avg-signal22.773933
Spike_AFFX-r2-Bs-thr_avg-signal20.374304
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1484.704956
Spike_AFFX-r2-Bs-phe_5_signal7.098246
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1777.851074
RawQ2.529737
Spike_AFFX-r2-Bs-lys_5_signal4.713979
Signal(A)5.517098
%A33.928101
Signal(All)140.251068
Corner+Avg:170,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal321.149872
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal16.530205
Spike_AFFX-r2-Ec-bioD_avg-signal1631.278076
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P64.274445
Spike_AFFX-r2-Bs-lys_avg-signal10.112287
Spike_AFFX-r2-P1-cre_avg-signal5404.224609
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.797457
Spike_AFFX-r2-Bs-thr_3_signal34.113655
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-signal10.033050
Spike_AFFX-r2-Bs-dap_3_signal88.228172
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.197444
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal342.126007
#M410
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal23.457083
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.938689
Spike_AFFX-r2-Bs-thr_M_signal21.334158
Signal(P)214.757629
Spike_AFFX-r2-Bs-phe_3-5-ratio2.328773
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7070,Count:9
Spike_AFFX-r2-P1-cre_5_signal5035.550781
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7739
Signal(M)19.191887
BackgroundAvg:64.39,Std:1.50,Min:60.4,Max:67.1
Spike_AFFX-r2-Ec-bioC_avg-signal331.637939
Spike_AFFX-r2-Bs-dap_avg-signal46.774414
Spike_AFFX-r2-Bs-dap_3-5-ratio5.936101
Spike_AFFX-r2-Ec-bioB_5_signal26.437141
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.823572
NF1.000000
HZ4
Tau0.015000

Slide: Yang_635-15_Dex_4h_buds_ms35 mutant_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 ("Yang_635-15_Dex_4h_buds_ms35 mutant_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: Yang_635-15_Dex_4h_buds_ms35 mutant_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: ms35 mutant
Stock Code:
Genetic Background: Ler
Growth Conditions:
ProtocolPlants were grown in growth rooms at 22h of daylight and 2h of night at 22 C; in 3x4 well tray with 2 plants per well
Soil ConstituentsCommercial soil: Levington M3 mixed with intercept(The Scotts Company, UK)
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
Medium
Lighting(Source: High pressure sodium and metal halide. Wavelength: White)0.366666666666667 hour days, 0.0333333333333333 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: X-rays induced mutation mutation in
Tissue: buds
in vivo Treatment: When plants flowering with 3-5 silique (5 weeks), 25uM Dex +0.02% Silwet was spayed onto infloroscences and covered with lid. All unopened flower buds from primary infloroscences of 5 plats were collected.
Additional Organism Information:
Sample DescriptionAll unopened flower buds from primary infloroscences of 5 plants were collected 4 hours after Dex treatment.
Other Information:
Timecourse start procedureWhen Dex was applied to plants

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:0.462263
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-ratio1.245897
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.968247
Spike_AFFX-r2-Bs-dap_5_signal22.892843
NoiseAvg:3.15,Std:0.07,Min:3.0,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal2.559291
#P15721
Spike_AFFX-r2-Bs-phe_M_signal7.214571
Corner-Avg:13351,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal8.268835
Spike_AFFX-r2-Ec-bioB_3_signal9.571979
Spike_AFFX-r2-Bs-lys_M_signal15.647556
Spike_AFFX-r2-P1-cre_3_signal3909.467773
Spike_AFFX-r2-Bs-lys_3-5-ratio1.823409
Spike_AFFX-r2-Bs-dap_M_signal60.932037
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio13.688313
Spike_AFFX-r2-Ec-bioB_avg-signal9.242233
Spike_AFFX-r2-Bs-thr_avg-signal18.192436
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal877.050415
Spike_AFFX-r2-Bs-phe_5_signal10.906771
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1157.263184
RawQ2.696628
Spike_AFFX-r2-Bs-lys_5_signal9.818812
Signal(A)3.845162
%A29.447611
Signal(All)134.724564
Corner+Avg:225,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal223.344849
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal12.797732
Spike_AFFX-r2-Ec-bioD_avg-signal1017.156799
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.921524
Spike_AFFX-r2-Bs-lys_avg-signal14.456695
Spike_AFFX-r2-P1-cre_avg-signal3523.671387
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.630864
Spike_AFFX-r2-Bs-thr_3_signal35.032383
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-signal10.306357
Spike_AFFX-r2-Bs-dap_3_signal120.220268
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.319494
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal200.828506
#M372
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal17.903715
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.112117
Spike_AFFX-r2-Bs-thr_M_signal16.985634
Signal(P)193.510590
Spike_AFFX-r2-Bs-phe_3-5-ratio1.173375
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10972,Count:9
Spike_AFFX-r2-P1-cre_5_signal3137.874756
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6717
Signal(M)13.600160
BackgroundAvg:68.92,Std:1.26,Min:65.0,Max:71.7
Spike_AFFX-r2-Ec-bioC_avg-signal212.086670
Spike_AFFX-r2-Bs-dap_avg-signal68.015053
Spike_AFFX-r2-Bs-dap_3-5-ratio5.251434
Spike_AFFX-r2-Ec-bioB_5_signal9.885886
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.462263
NF1.000000
HZ4
Tau0.015000

Slide: Yang_635-14_Dex_2h_buds_ms35 mutant_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 ("Yang_635-14_Dex_2h_buds_ms35 mutant_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: Yang_635-14_Dex_2h_buds_ms35 mutant_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: ms35 mutant
Stock Code:
Genetic Background: Ler
Growth Conditions:
ProtocolPlants were grown in growth rooms at 22h of daylight and 2h of night at 22 C; in 3x4 well tray with 2 plants per well
Soil ConstituentsCommercial soil: Levington M3 mixed with intercept(The Scotts Company, UK)
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
Medium
Lighting(Source: High pressure sodium and metal halide. Wavelength: White)0.366666666666667 hour days, 0.0333333333333333 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: X-rays induced mutation mutation in
Tissue: buds
in vivo Treatment: When plants flowering with 3-5 silique (5 weeks), 25uM Dex +0.02% Silwet was spayed onto infloroscences and covered with lid. All unopened flower buds from primary infloroscences of 5 plats were collected.
Additional Organism Information:
Sample DescriptionAll unopened flower buds from primary infloroscences of 5 plants were collected 2 hours after Dex treatment.
Other Information:
Timecourse start procedureWhen Dex was applied to plants

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:0.529032
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-ratio1.107569
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.925382
Spike_AFFX-r2-Bs-dap_5_signal19.541485
NoiseAvg:3.17,Std:0.13,Min:2.8,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_signal4.971450
#P15149
Spike_AFFX-r2-Bs-phe_M_signal14.230226
Corner-Avg:13281,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal17.133743
Spike_AFFX-r2-Ec-bioB_3_signal21.248528
Spike_AFFX-r2-Bs-lys_M_signal10.468551
Spike_AFFX-r2-P1-cre_3_signal4565.256348
Spike_AFFX-r2-Bs-lys_3-5-ratio3.074817
Spike_AFFX-r2-Bs-dap_M_signal45.250175
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.041862
Spike_AFFX-r2-Ec-bioB_avg-signal20.448053
Spike_AFFX-r2-Bs-thr_avg-signal20.530802
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1250.428101
Spike_AFFX-r2-Bs-phe_5_signal6.099633
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1606.491455
RawQ2.700672
Spike_AFFX-r2-Bs-lys_5_signal7.618746
Signal(A)4.301837
%A31.823761
Signal(All)139.450394
Corner+Avg:229,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal298.520569
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal12.570305
Spike_AFFX-r2-Ec-bioD_avg-signal1428.459717
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.413857
Spike_AFFX-r2-Bs-lys_avg-signal13.837850
Spike_AFFX-r2-P1-cre_avg-signal4343.564453
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.762385
Spike_AFFX-r2-Bs-thr_3_signal39.979717
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionM
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal10.966721
Spike_AFFX-r2-Bs-dap_3_signal111.438721
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.284753
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal258.012726
#M402
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.426252
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.156999
Spike_AFFX-r2-Bs-thr_M_signal16.641239
Signal(P)207.462112
Spike_AFFX-r2-Bs-phe_3-5-ratio2.060830
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11105,Count:9
Spike_AFFX-r2-P1-cre_5_signal4121.872070
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7259
Signal(M)16.898293
BackgroundAvg:70.98,Std:1.20,Min:67.5,Max:73.0
Spike_AFFX-r2-Ec-bioC_avg-signal278.266663
Spike_AFFX-r2-Bs-dap_avg-signal58.743465
Spike_AFFX-r2-Bs-dap_3-5-ratio5.702674
Spike_AFFX-r2-Ec-bioB_5_signal22.961887
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.529032
NF1.000000
HZ4
Tau0.015000

Slide: Yang_635-13_Dex_0h_buds_ms35 mutant_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 ("Yang_635-13_Dex_0h_buds_ms35 mutant_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: Yang_635-13_Dex_0h_buds_ms35 mutant_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: ms35 mutant
Stock Code:
Genetic Background: Ler
Growth Conditions:
ProtocolPlants were grown in growth rooms at 22h of daylight and 2h of night at 22 C; in 3x4 well tray with 2 plants per well
Soil ConstituentsCommercial soil: Levington M3 mixed with intercept(The Scotts Company, UK)
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
Medium
Lighting(Source: High pressure sodium and metal halide. Wavelength: White)0.366666666666667 hour days, 0.0333333333333333 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: X-rays induced mutation mutation in
Tissue: buds
Additional Organism Information:
Sample DescriptionAll unopened flower buds from primary infloroscences of 5 plants were collected just before Dex treatment.
Other Information:
Timecourse start procedureJust before Dex was applied to plants

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:0.55125
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-ratio1.210911
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.135011
Spike_AFFX-r2-Bs-dap_5_signal15.152256
NoiseAvg:2.92,Std:0.11,Min:2.5,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_signal0.509971
#P15404
Spike_AFFX-r2-Bs-phe_M_signal15.095635
Corner-Avg:12772,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal17.586500
Spike_AFFX-r2-Ec-bioB_3_signal20.138500
Spike_AFFX-r2-Bs-lys_M_signal10.595808
Spike_AFFX-r2-P1-cre_3_signal4695.160156
Spike_AFFX-r2-Bs-lys_3-5-ratio2.402416
Spike_AFFX-r2-Bs-dap_M_signal62.496605
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio41.504162
Spike_AFFX-r2-Ec-bioB_avg-signal18.489332
Spike_AFFX-r2-Bs-thr_avg-signal19.700899
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1169.950806
Spike_AFFX-r2-Bs-phe_5_signal3.798230
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1503.379150
RawQ2.625453
Spike_AFFX-r2-Bs-lys_5_signal12.048130
Signal(A)4.160095
%A30.881193
Signal(All)137.338409
Corner+Avg:214,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal296.602936
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal12.541345
Spike_AFFX-r2-Ec-bioD_avg-signal1336.665039
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P67.531784
Spike_AFFX-r2-Bs-lys_avg-signal17.196186
Spike_AFFX-r2-P1-cre_avg-signal4286.269531
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.587023
Spike_AFFX-r2-Bs-thr_3_signal41.504162
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-signal10.478404
Spike_AFFX-r2-Bs-dap_3_signal122.674103
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.284994
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal267.028564
#M362
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.944620
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.110754
Spike_AFFX-r2-Bs-thr_M_signal17.088566
Signal(P)201.102341
Spike_AFFX-r2-Bs-phe_3-5-ratio3.301892
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10426,Count:9
Spike_AFFX-r2-P1-cre_5_signal3877.379150
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7044
Signal(M)15.483435
BackgroundAvg:62.27,Std:0.44,Min:61.1,Max:63.7
Spike_AFFX-r2-Ec-bioC_avg-signal281.815735
Spike_AFFX-r2-Bs-dap_avg-signal66.774323
Spike_AFFX-r2-Bs-dap_3-5-ratio8.096095
Spike_AFFX-r2-Ec-bioB_5_signal17.743000
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.551250
NF1.000000
HZ4
Tau0.015000

Slide: Yang_635-12_Dex _6h_buds_MYB26-ms35_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 ("Yang_635-12_Dex _6h_buds_MYB26-ms35_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: Yang_635-12_Dex _6h_buds_MYB26-ms35_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: ms35 transformed with MYB26pro:MYB26 GRYFP
Stock Code:
Genetic Background: Ler
Growth Conditions:
ProtocolPlants were grown in growth rooms at 22h of daylight and 2h of night at 22 C; in 3x4 well tray with 2 plants per well
Soil ConstituentsCommercial soil: Levington M3 mixed with intercept(The Scotts Company, UK)
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
Medium
Lighting(Source: High pressure sodium and metal halide. Wavelength: White)0.366666666666667 hour days, 0.0333333333333333 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: X-rays induced mutation mutation in
Tissue: buds
in vivo Treatment: When plants flowering with 3-5 silique (5 weeks), 25uM Dex +0.02% Silwet was spayed onto infloroscences and covered with lid. All unopened flower buds from primary infloroscences of 5 plats were collected.
Additional Organism Information:
Sample DescriptionAll unopened flower buds from primary infloroscences of 5 plants were collected at 6 hours after Dex treatment.
Other Information:
Timecourse start procedurewhen Dex was applied to plants

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:0.74024
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-ratio1.299247
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.405127
Spike_AFFX-r2-Bs-dap_5_signal20.725309
NoiseAvg:2.59,Std:0.11,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_signal6.550763
#P14999
Spike_AFFX-r2-Bs-phe_M_signal11.823398
Corner-Avg:11194,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal18.259842
Spike_AFFX-r2-Ec-bioB_3_signal11.828071
Spike_AFFX-r2-Bs-lys_M_signal16.635485
Spike_AFFX-r2-P1-cre_3_signal6818.094727
Spike_AFFX-r2-Bs-lys_3-5-ratio3.229441
Spike_AFFX-r2-Bs-dap_M_signal50.756084
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.092060
Spike_AFFX-r2-Ec-bioB_avg-signal19.761284
Spike_AFFX-r2-Bs-thr_avg-signal27.335098
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1605.802734
Spike_AFFX-r2-Bs-phe_5_signal11.669466
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1839.180542
RawQ2.427654
Spike_AFFX-r2-Bs-lys_5_signal10.229863
Signal(A)4.572779
%A32.481369
Signal(All)141.096664
Corner+Avg:190,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal346.265381
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal14.632312
Spike_AFFX-r2-Ec-bioD_avg-signal1722.491699
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.756248
Spike_AFFX-r2-Bs-lys_avg-signal19.967363
Spike_AFFX-r2-P1-cre_avg-signal6032.910645
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.762385
Spike_AFFX-r2-Bs-thr_3_signal53.009167
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-signal12.708392
Spike_AFFX-r2-Bs-dap_3_signal142.862564
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.145334
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal307.617828
#M402
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal33.036743
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.125635
Spike_AFFX-r2-Bs-thr_M_signal22.445366
Signal(P)211.844513
Spike_AFFX-r2-Bs-phe_3-5-ratio1.253897
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9292,Count:9
Spike_AFFX-r2-P1-cre_5_signal5247.726563
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7409
Signal(M)17.610312
BackgroundAvg:62.09,Std:1.43,Min:59.9,Max:65.5
Spike_AFFX-r2-Ec-bioC_avg-signal326.941589
Spike_AFFX-r2-Bs-dap_avg-signal71.447990
Spike_AFFX-r2-Bs-dap_3-5-ratio6.893145
Spike_AFFX-r2-Ec-bioB_5_signal29.195940
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.740240
NF1.000000
HZ4
Tau0.015000


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