NASC's International Affymetrix Service

AI logo

NASCArrays

home, selection, spot history, gene swinger, two gene scatterplot, digital northern, bulk gene download, tutorial, help, Affymetrix site, NASC

Experiment: DELLA-mediated regulation of seedling trascriptome

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-587

Seedling growth in short days shows a rhythmic pattern occurring mostly at the end of the night. The increase in growth rate is related with changes in the expression of PIF4, PIF5 and several phytohormone genes as well as with an increment in auxin signaling in the seedling (Nozue, Covington et al. 2006; Covington and Harmer 2007; Michael, Breton et al. 2008).

Gibberellins (GA) are main promoters of hypocotyl elongation, and the way in which they contribute to rhythmic growth is still unknown.We found that in short day grown seedlings, DELLA proteins accumulate during the day and show a minimum at the middle of the night, shortly before the period when hypocotyl growth increases. The circadian clock regulates the transcript level of two GA receptor genes; GID1A and GID1B. Changes in DELLA accumulation are associated with GID1s expression, indicating that DELLA proteins oscillation in the seedlings is regulated, at least in part, by the clock-mediated control of GID1s. The decrease in DELLA proteins at the end of the night is relevant for proper hypocotyl growth.

In order to study the way in which DELLA oscillations contribute to rhythmic patterns of growth we performed transcriptome analysis of wild type and quintuple della mutant seedlings grown under SD.

Samples were taken in two periods of the night: shortly after the dark period starts (ZT9), characterized by a strong DELLA accumulation and low growth rate, and near the end of the night (ZT21) where the opposite pattern is observed. Genes exhibiting a diurnal oscillation in circadian gene expression databases (e.g. Diurnal: http://diurnal.cgrb.oregonstate.edu/) and show a different pattern of regulation in della mutants compared with the wild type early in the night will be chosen for diurnal expression studies and functional analysis.

References

Covington, M. and S. Harmer (2007).

"The Circadian Clock Regulates Auxin Signaling and Responses in Arabidopsis.

"PLOS Biology 8: 1773-1784.Michael, T., G. Breton, et al. (2008).

"A morning-specific phytohormone gene expression program underlying rhythmic plant growth.

"PLOS Biology 6(9): e225. doi:10.1371/journal.pbio.0060225.

Nozue, K., M. Covington, et al. (2006).

"Rhythmic growth explained by coincidence between internal and external cues.

"Nature(448): 358-363.

About the Experimenter

Name:Dr David Alabadi
Head of Lab Name:Dr David Alabadi
Lab:
Address:Departamento de Biologia del Desarrollo, Instituto de Biologia Molecular y Celular de Plantas - CSIC, Universidad Politecnica de Valencia
Avenida de los Naranjos s/n, Valencia, , 46022, SPAIN
Postcode:
Country:
 
Telephone Number: 34963877786
Fax Number: 34963877859

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: time_series_design; genetic_modification_design
Number of Slides:12
 
Experimental Parameters:
parameter timepoint
parametergene_knock_out
Quality Control Measures Taken:
biological-replicates3
References:
referenceArana MV, Marín-de la Rosa N, Maloof JN, Blázquez MA, Alabadí D. Circadian oscillation of gibberellin signaling in Arabidopsis. Proc Natl Acad Sci U S A. 2011;108:9292–9297
 
Other Information:

Slides in this Experiment

Hybridisation Set: Alabadi: DELLA-mediated regulation of seedling trascriptome

Slide: Arana_587-6_Ler-21hrs_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Arana_587-6_Ler-21hrs_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Arana_587-6_Ler-21hrs_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 5 days old
Growth Conditions:
StratificationSeeds were stratified for 4 days in MS (Murashige & Skoog medium) including modified vitamins, Duchefa Biuochemie.
SterilisationSurface- sterilized with 10 min in 1 ml ethanol 70% Triton 0,05% followed by 7 min in ETOH 96%.
ProtocolSeedlings were grown under photoperiodic conditions; 8h white light, 16 h darkness. Light intensity: 200 µE. Continuous temperature: 22 °C, 50% humidity for 5 days. Medium: MS with modified vitamins.
Percentage Agrose8
Substrate Sterilising Procedureautoclave 20 min
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent. Intensity: 200µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample Description5 days old whole seedlings
Other Information:
Timecourse start procedureTime 0 is the moment in which the lights are on, and the “day” starts.

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:0.734929
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-ratio1.115244
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.214526
Spike_AFFX-r2-Bs-dap_5_signal263.419159
NoiseAvg:2.36,Std:0.07,Min:2.1,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_signal83.130257
#P14261
Spike_AFFX-r2-Bs-phe_M_signal82.485298
Corner-Avg:12059,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal131.515305
Spike_AFFX-r2-Ec-bioB_3_signal109.142754
Spike_AFFX-r2-Bs-lys_M_signal31.634367
Spike_AFFX-r2-P1-cre_3_signal5076.419434
Spike_AFFX-r2-Bs-lys_3-5-ratio1.847513
Spike_AFFX-r2-Bs-dap_M_signal503.016205
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.806401
Spike_AFFX-r2-Ec-bioB_avg-signal110.174187
Spike_AFFX-r2-Bs-thr_avg-signal204.002869
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1097.402344
Spike_AFFX-r2-Bs-phe_5_signal67.873703
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1651.844116
RawQ2.279072
Spike_AFFX-r2-Bs-lys_5_signal52.629204
Signal(A)4.806754
%A35.453747
Signal(All)148.830490
Corner+Avg:105,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal431.340149
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal141.796997
Spike_AFFX-r2-Ec-bioD_avg-signal1374.623291
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.520824
Spike_AFFX-r2-Bs-lys_avg-signal60.498913
Spike_AFFX-r2-P1-cre_avg-signal4814.131836
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.025427
Spike_AFFX-r2-Bs-thr_3_signal316.427124
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-signal97.385338
Spike_AFFX-r2-Bs-dap_3_signal686.984070
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.505231
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal346.307495
#M462
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal97.233154
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.245541
Spike_AFFX-r2-Bs-thr_M_signal212.451248
Signal(P)234.757614
Spike_AFFX-r2-Bs-phe_3-5-ratio2.089130
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9808,Count:9
Spike_AFFX-r2-P1-cre_5_signal4551.844727
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8087
Signal(M)17.474312
BackgroundAvg:55.04,Std:0.56,Min:53.4,Max:56.2
Spike_AFFX-r2-Ec-bioC_avg-signal388.823822
Spike_AFFX-r2-Bs-dap_avg-signal484.473145
Spike_AFFX-r2-Bs-dap_3-5-ratio2.607950
Spike_AFFX-r2-Ec-bioB_5_signal89.864494
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.734929
NF1.000000
HZ4
Tau0.015000

Slide: Arana_587-5_Ler-21hrs_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 ("Arana_587-5_Ler-21hrs_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: Arana_587-5_Ler-21hrs_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 5 days old
Growth Conditions:
StratificationSeeds were stratified for 4 days in MS (Murashige & Skoog medium) including modified vitamins, Duchefa Biuochemie.
SterilisationSurface- sterilized with 10 min in 1 ml ethanol 70% Triton 0,05% followed by 7 min in ETOH 96%.
ProtocolSeedlings were grown under photoperiodic conditions; 8h white light, 16 h darkness. Light intensity: 200 µE. Continuous temperature: 22 °C, 50% humidity for 5 days. Medium: MS with modified vitamins.
Percentage Agrose8
Substrate Sterilising Procedureautoclave 20 min
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent. Intensity: 200µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample Description5 days old whole seedlings
Other Information:
Timecourse start procedureTime 0 is the moment in which the lights are on, and the “day” starts.

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:0.841577
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-ratio1.181397
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.425374
Spike_AFFX-r2-Bs-dap_5_signal294.976532
NoiseAvg:2.59,Std:0.09,Min:2.3,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_signal86.950882
#P13710
Spike_AFFX-r2-Bs-phe_M_signal98.342461
Corner-Avg:10177,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal109.904968
Spike_AFFX-r2-Ec-bioB_3_signal77.161018
Spike_AFFX-r2-Bs-lys_M_signal51.082916
Spike_AFFX-r2-P1-cre_3_signal4945.776367
Spike_AFFX-r2-Bs-lys_3-5-ratio2.547597
Spike_AFFX-r2-Bs-dap_M_signal584.217224
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.231206
Spike_AFFX-r2-Ec-bioB_avg-signal80.399956
Spike_AFFX-r2-Bs-thr_avg-signal316.350128
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal874.609009
Spike_AFFX-r2-Bs-phe_5_signal93.970490
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1570.510498
RawQ2.399995
Spike_AFFX-r2-Bs-lys_5_signal50.963806
Signal(A)5.462865
%A37.843052
Signal(All)146.067307
Corner+Avg:96,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal309.436096
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal161.064514
Spike_AFFX-r2-Ec-bioD_avg-signal1222.559814
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.105217
Spike_AFFX-r2-Bs-lys_avg-signal77.293983
Spike_AFFX-r2-P1-cre_avg-signal4566.078125
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.051732
Spike_AFFX-r2-Bs-thr_3_signal541.808899
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-signal117.792488
Spike_AFFX-r2-Bs-dap_3_signal802.322266
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.795672
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal298.493530
#M468
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal129.835220
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.036659
Spike_AFFX-r2-Bs-thr_M_signal320.290558
Signal(P)238.939102
Spike_AFFX-r2-Bs-phe_3-5-ratio1.713990
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7313,Count:9
Spike_AFFX-r2-P1-cre_5_signal4186.380371
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8632
Signal(M)18.770590
BackgroundAvg:57.67,Std:0.34,Min:56.9,Max:59.0
Spike_AFFX-r2-Ec-bioC_avg-signal303.964813
Spike_AFFX-r2-Bs-dap_avg-signal560.505371
Spike_AFFX-r2-Bs-dap_3-5-ratio2.719953
Spike_AFFX-r2-Ec-bioB_5_signal54.133888
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.841577
NF1.000000
HZ4
Tau0.015000

Slide: Arana_587-4_Ler-21hrs_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 ("Arana_587-4_Ler-21hrs_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: Arana_587-4_Ler-21hrs_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 5 days old
Growth Conditions:
StratificationSeeds were stratified for 4 days in MS (Murashige & Skoog medium) including modified vitamins, Duchefa Biuochemie.
SterilisationSurface- sterilized with 10 min in 1 ml ethanol 70% Triton 0,05% followed by 7 min in ETOH 96%.
ProtocolSeedlings were grown under photoperiodic conditions; 8h white light, 16 h darkness. Light intensity: 200 µE. Continuous temperature: 22 °C, 50% humidity for 5 days. Medium: MS with modified vitamins.
Percentage Agrose8
Substrate Sterilising Procedureautoclave 20 min
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent. Intensity: 200µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample Description5 days old whole seedlings
Other Information:
Timecourse start procedureTime 0 is the moment in which the lights are on, and the “day” starts.

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:0.826412
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-ratio1.215423
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.155676
Spike_AFFX-r2-Bs-dap_5_signal236.174957
NoiseAvg:1.88,Std:0.07,Min:1.7,Max:2.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal97.215347
#P13988
Spike_AFFX-r2-Bs-phe_M_signal82.970734
Corner-Avg:12512,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal178.463943
Spike_AFFX-r2-Ec-bioB_3_signal141.633972
Spike_AFFX-r2-Bs-lys_M_signal40.160217
Spike_AFFX-r2-P1-cre_3_signal7536.665039
Spike_AFFX-r2-Bs-lys_3-5-ratio1.470245
Spike_AFFX-r2-Bs-dap_M_signal469.158722
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.583210
Spike_AFFX-r2-Ec-bioB_avg-signal147.551010
Spike_AFFX-r2-Bs-thr_avg-signal215.928101
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1802.357422
Spike_AFFX-r2-Bs-phe_5_signal68.711098
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2571.275391
RawQ1.984941
Spike_AFFX-r2-Bs-lys_5_signal50.893520
Signal(A)4.738035
%A36.812801
Signal(All)154.547546
Corner+Avg:102,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal481.087219
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal152.415848
Spike_AFFX-r2-Ec-bioD_avg-signal2186.816406
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.323982
Spike_AFFX-r2-Bs-lys_avg-signal55.293217
Spike_AFFX-r2-P1-cre_avg-signal6868.762695
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.863218
Spike_AFFX-r2-Bs-thr_3_signal348.343048
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-signal101.365898
Spike_AFFX-r2-Bs-dap_3_signal711.487549
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.426618
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal478.346741
#M425
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal74.825920
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.005729
Spike_AFFX-r2-Bs-thr_M_signal202.225937
Signal(P)248.629181
Spike_AFFX-r2-Bs-phe_3-5-ratio2.218213
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8241,Count:9
Spike_AFFX-r2-P1-cre_5_signal6200.860352
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8397
Signal(M)17.927593
BackgroundAvg:67.52,Std:0.27,Min:67.0,Max:68.4
Spike_AFFX-r2-Ec-bioC_avg-signal479.716980
Spike_AFFX-r2-Bs-dap_avg-signal472.273712
Spike_AFFX-r2-Bs-dap_3-5-ratio3.012544
Spike_AFFX-r2-Ec-bioB_5_signal122.555107
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.826412
NF1.000000
HZ4
Tau0.015000

Slide: Arana_587-3_Ler-9hrs_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Arana_587-3_Ler-9hrs_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Arana_587-3_Ler-9hrs_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 5 days old
Growth Conditions:
StratificationSeeds were stratified for 4 days in MS (Murashige & Skoog medium) including modified vitamins, Duchefa Biuochemie.
SterilisationSurface- sterilized with 10 min in 1 ml ethanol 70% Triton 0,05% followed by 7 min in ETOH 96%.
ProtocolSeedlings were grown under photoperiodic conditions; 8h white light, 16 h darkness. Light intensity: 200 µE. Continuous temperature: 22 °C, 50% humidity for 5 days. Medium: MS with modified vitamins.
Percentage Agrose8
Substrate Sterilising Procedureautoclave 20 min
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent. Intensity: 200µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample Description5 days old whole seedlings
Other Information:
Timecourse start procedureTime 0 is the moment in which the lights are on, and the “day” starts.

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:0.677456
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-ratio1.330923
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.313884
Spike_AFFX-r2-Bs-dap_5_signal350.369202
NoiseAvg:2.45,Std:0.09,Min:2.2,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_signal124.417038
#P14799
Spike_AFFX-r2-Bs-phe_M_signal130.295578
Corner-Avg:11515,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal104.017006
Spike_AFFX-r2-Ec-bioB_3_signal96.806320
Spike_AFFX-r2-Bs-lys_M_signal57.771381
Spike_AFFX-r2-P1-cre_3_signal5508.200684
Spike_AFFX-r2-Bs-lys_3-5-ratio1.019163
Spike_AFFX-r2-Bs-dap_M_signal715.341736
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.417020
Spike_AFFX-r2-Ec-bioB_avg-signal91.500954
Spike_AFFX-r2-Bs-thr_avg-signal311.170013
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal990.479004
Spike_AFFX-r2-Bs-phe_5_signal127.842972
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1576.427734
RawQ2.270816
Spike_AFFX-r2-Bs-lys_5_signal91.261040
Signal(A)4.228440
%A33.397633
Signal(All)144.323822
Corner+Avg:99,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal352.395813
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal254.322083
Spike_AFFX-r2-Ec-bioD_avg-signal1283.453369
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.879440
Spike_AFFX-r2-Bs-lys_avg-signal80.680756
Spike_AFFX-r2-P1-cre_avg-signal4823.416992
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_signal549.552612
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-signal170.820206
Spike_AFFX-r2-Bs-dap_3_signal868.180054
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.591581
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal328.380005
#M393
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal93.009842
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.073134
Spike_AFFX-r2-Bs-thr_M_signal259.540436
Signal(P)219.862625
Spike_AFFX-r2-Bs-phe_3-5-ratio1.989332
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9458,Count:9
Spike_AFFX-r2-P1-cre_5_signal4138.632813
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7618
Signal(M)15.437670
BackgroundAvg:79.35,Std:0.56,Min:77.4,Max:80.5
Spike_AFFX-r2-Ec-bioC_avg-signal340.387909
Spike_AFFX-r2-Bs-dap_avg-signal644.630310
Spike_AFFX-r2-Bs-dap_3-5-ratio2.477901
Spike_AFFX-r2-Ec-bioB_5_signal73.679520
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.677456
NF1.000000
HZ4
Tau0.015000

Slide: Arana_587-2_Ler-9hrs_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 ("Arana_587-2_Ler-9hrs_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: Arana_587-2_Ler-9hrs_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 5 days old
Growth Conditions:
StratificationSeeds were stratified for 4 days in MS (Murashige & Skoog medium) including modified vitamins, Duchefa Biuochemie.
SterilisationSurface- sterilized with 10 min in 1 ml ethanol 70% Triton 0,05% followed by 7 min in ETOH 96%.
ProtocolSeedlings were grown under photoperiodic conditions; 8h white light, 16 h darkness. Light intensity: 200 µE. Continuous temperature: 22 °C, 50% humidity for 5 days. Medium: MS with modified vitamins.
Percentage Agrose8
Substrate Sterilising Procedureautoclave 20 min
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent. Intensity: 200µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample Description5 days old whole seedlings
Other Information:
Timecourse start procedureTime 0 is the moment in which the lights are on, and the “day” starts.

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:0.760725
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-ratio1.218122
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.782714
Spike_AFFX-r2-Bs-dap_5_signal176.197098
NoiseAvg:2.12,Std:0.06,Min:2.0,Max:2.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal56.913162
#P14336
Spike_AFFX-r2-Bs-phe_M_signal71.404839
Corner-Avg:10598,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal124.607208
Spike_AFFX-r2-Ec-bioB_3_signal128.705765
Spike_AFFX-r2-Bs-lys_M_signal36.589436
Spike_AFFX-r2-P1-cre_3_signal6112.878906
Spike_AFFX-r2-Bs-lys_3-5-ratio1.876328
Spike_AFFX-r2-Bs-dap_M_signal410.286346
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.411813
Spike_AFFX-r2-Ec-bioB_avg-signal108.503174
Spike_AFFX-r2-Bs-thr_avg-signal172.832718
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1210.887817
Spike_AFFX-r2-Bs-phe_5_signal67.588234
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1934.702393
RawQ2.010227
Spike_AFFX-r2-Bs-lys_5_signal38.344398
Signal(A)4.497490
%A35.374836
Signal(All)150.422989
Corner+Avg:84,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal370.821686
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal128.902344
Spike_AFFX-r2-Ec-bioD_avg-signal1572.795166
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.849628
Spike_AFFX-r2-Bs-lys_avg-signal48.960175
Spike_AFFX-r2-P1-cre_avg-signal5565.580566
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.775537
Spike_AFFX-r2-Bs-thr_3_signal308.003387
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-signal89.298470
Spike_AFFX-r2-Bs-dap_3_signal609.674194
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.597755
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal364.184448
#M405
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal71.946678
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.018225
Spike_AFFX-r2-Bs-thr_M_signal153.581619
Signal(P)236.337524
Spike_AFFX-r2-Bs-phe_3-5-ratio1.907171
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8315,Count:9
Spike_AFFX-r2-P1-cre_5_signal5018.282227
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8069
Signal(M)16.601336
BackgroundAvg:72.24,Std:0.53,Min:70.8,Max:73.7
Spike_AFFX-r2-Ec-bioC_avg-signal367.503052
Spike_AFFX-r2-Bs-dap_avg-signal398.719238
Spike_AFFX-r2-Bs-dap_3-5-ratio3.460183
Spike_AFFX-r2-Ec-bioB_5_signal72.196541
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.760725
NF1.000000
HZ4
Tau0.015000

Slide: Arana_587-1_Ler-9hrs_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 ("Arana_587-1_Ler-9hrs_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: Arana_587-1_Ler-9hrs_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 5 days old
Growth Conditions:
StratificationSeeds were stratified for 4 days in MS (Murashige & Skoog medium) including modified vitamins, Duchefa Biuochemie.
SterilisationSurface- sterilized with 10 min in 1 ml ethanol 70% Triton 0,05% followed by 7 min in ETOH 96%.
ProtocolSeedlings were grown under photoperiodic conditions; 8h white light, 16 h darkness. Light intensity: 200 µE. Continuous temperature: 22 °C, 50% humidity for 5 days. Medium: MS with modified vitamins.
Percentage Agrose8
Substrate Sterilising Procedureautoclave 20 min
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent. Intensity: 200µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample Description5 days old whole seedlings
Other Information:
Timecourse start procedureTime 0 is the moment in which the lights are on, and the “day” starts.

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:0.468276
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-ratio1.258982
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.248662
Spike_AFFX-r2-Bs-dap_5_signal219.839447
NoiseAvg:2.72,Std:0.06,Min:2.6,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_signal68.249336
#P15056
Spike_AFFX-r2-Bs-phe_M_signal73.544662
Corner-Avg:14343,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal110.301056
Spike_AFFX-r2-Ec-bioB_3_signal99.046631
Spike_AFFX-r2-Bs-lys_M_signal32.640049
Spike_AFFX-r2-P1-cre_3_signal4775.885254
Spike_AFFX-r2-Bs-lys_3-5-ratio1.708081
Spike_AFFX-r2-Bs-dap_M_signal493.417633
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.733464
Spike_AFFX-r2-Ec-bioB_avg-signal96.223297
Spike_AFFX-r2-Bs-thr_avg-signal153.065659
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal985.681946
Spike_AFFX-r2-Bs-phe_5_signal73.257683
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1438.083496
RawQ2.453315
Spike_AFFX-r2-Bs-lys_5_signal42.433807
Signal(A)3.762404
%A32.174484
Signal(All)144.328033
Corner+Avg:145,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal319.688477
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal148.067505
Spike_AFFX-r2-Ec-bioD_avg-signal1211.882690
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.006134
Spike_AFFX-r2-Bs-lys_avg-signal49.184742
Spike_AFFX-r2-P1-cre_avg-signal4284.667969
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.819377
Spike_AFFX-r2-Bs-thr_3_signal254.806473
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-signal98.289948
Spike_AFFX-r2-Bs-dap_3_signal612.077637
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.458973
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal284.202148
#M415
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal72.480370
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.124863
Spike_AFFX-r2-Bs-thr_M_signal136.141144
Signal(P)216.425781
Spike_AFFX-r2-Bs-phe_3-5-ratio2.021187
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11643,Count:9
Spike_AFFX-r2-P1-cre_5_signal3793.451172
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7339
Signal(M)14.466509
BackgroundAvg:61.30,Std:1.04,Min:57.9,Max:63.5
Spike_AFFX-r2-Ec-bioC_avg-signal301.945313
Spike_AFFX-r2-Bs-dap_avg-signal441.778229
Spike_AFFX-r2-Bs-dap_3-5-ratio2.784203
Spike_AFFX-r2-Ec-bioB_5_signal79.322205
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.468276
NF1.000000
HZ4
Tau0.015000

Slide: Arana_587-7_della-9hrs_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 ("Arana_587-7_della-9hrs_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: Arana_587-7_della-9hrs_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: della
Stock Code: N16298
Genetic Background: Ler(Landsberg_erecta)
Age: 5 days old
Growth Conditions:
StratificationSeeds were stratified for 4 days in MS (Murashige & Skoog medium) including modified vitamins, Duchefa Biuochemie.
SterilisationSurface- sterilized with 10 min in 1 ml ethanol 70% Triton 0,05% followed by 7 min in ETOH 96%.
ProtocolSeedlings were grown under photoperiodic conditions; 8h white light, 16 h darkness. Light intensity: 200 µE. Continuous temperature: 22 °C, 50% humidity for 5 days. Medium: MS with modified vitamins.
Percentage Agrose8
Substrate Sterilising Procedureautoclave 20 min
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent. Intensity: 200µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: transposon insertion
Tissue: whole plant
Additional Organism Information:
Sample Description5 days old whole seedlings
Other Information:
Timecourse start procedureTime 0 is the moment in which the lights are on, and the “day” starts.

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:0.746353
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-ratio1.235073
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.584315
Spike_AFFX-r2-Bs-dap_5_signal240.252518
NoiseAvg:2.51,Std:0.07,Min:2.3,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal74.979286
#P14320
Spike_AFFX-r2-Bs-phe_M_signal77.470680
Corner-Avg:12347,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal111.251526
Spike_AFFX-r2-Ec-bioB_3_signal109.251633
Spike_AFFX-r2-Bs-lys_M_signal34.677162
Spike_AFFX-r2-P1-cre_3_signal5533.913574
Spike_AFFX-r2-Bs-lys_3-5-ratio1.731207
Spike_AFFX-r2-Bs-dap_M_signal506.114410
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.460470
Spike_AFFX-r2-Ec-bioB_avg-signal96.487144
Spike_AFFX-r2-Bs-thr_avg-signal207.340149
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1006.302490
Spike_AFFX-r2-Bs-phe_5_signal53.751099
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1658.125854
RawQ2.332370
Spike_AFFX-r2-Bs-lys_5_signal50.398476
Signal(A)5.528207
%A35.256466
Signal(All)149.222412
Corner+Avg:108,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal402.792480
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal136.580017
Spike_AFFX-r2-Ec-bioD_avg-signal1332.214111
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.779484
Spike_AFFX-r2-Bs-lys_avg-signal57.441944
Spike_AFFX-r2-P1-cre_avg-signal5007.275391
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.964051
Spike_AFFX-r2-Bs-thr_3_signal334.442841
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-signal89.267265
Spike_AFFX-r2-Bs-dap_3_signal644.383240
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.647741
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal321.529938
#M448
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal87.250191
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.252737
Spike_AFFX-r2-Bs-thr_M_signal212.598328
Signal(P)234.010254
Spike_AFFX-r2-Bs-phe_3-5-ratio2.540972
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9904,Count:9
Spike_AFFX-r2-P1-cre_5_signal4480.637695
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8042
Signal(M)18.479233
BackgroundAvg:54.45,Std:1.05,Min:50.9,Max:56.3
Spike_AFFX-r2-Ec-bioC_avg-signal362.161194
Spike_AFFX-r2-Bs-dap_avg-signal463.583405
Spike_AFFX-r2-Bs-dap_3-5-ratio2.682108
Spike_AFFX-r2-Ec-bioB_5_signal68.958267
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.746353
NF1.000000
HZ4
Tau0.015000

Slide: Arana_587-8_della-9hrs_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 ("Arana_587-8_della-9hrs_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: Arana_587-8_della-9hrs_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: della
Stock Code: N16298
Genetic Background: Ler(Landsberg_erecta)
Age: 5 days old
Growth Conditions:
StratificationSeeds were stratified for 4 days in MS (Murashige & Skoog medium) including modified vitamins, Duchefa Biuochemie.
SterilisationSurface- sterilized with 10 min in 1 ml ethanol 70% Triton 0,05% followed by 7 min in ETOH 96%.
ProtocolSeedlings were grown under photoperiodic conditions; 8h white light, 16 h darkness. Light intensity: 200 µE. Continuous temperature: 22 °C, 50% humidity for 5 days. Medium: MS with modified vitamins.
Percentage Agrose8
Substrate Sterilising Procedureautoclave 20 min
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent. Intensity: 200µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: transposon insertion
Tissue: whole plant
Additional Organism Information:
Sample Description5 days old whole seedlings
Other Information:
Timecourse start procedureTime 0 is the moment in which the lights are on, and the “day” starts.

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:0.760294
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-ratio1.366917
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.087614
Spike_AFFX-r2-Bs-dap_5_signal165.690247
NoiseAvg:2.49,Std:0.11,Min:2.3,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_signal56.301338
#P14126
Spike_AFFX-r2-Bs-phe_M_signal52.833633
Corner-Avg:10011,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal89.766472
Spike_AFFX-r2-Ec-bioB_3_signal71.742531
Spike_AFFX-r2-Bs-lys_M_signal22.388239
Spike_AFFX-r2-P1-cre_3_signal4987.430176
Spike_AFFX-r2-Bs-lys_3-5-ratio1.296813
Spike_AFFX-r2-Bs-dap_M_signal391.047180
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.246379
Spike_AFFX-r2-Ec-bioB_avg-signal75.824089
Spike_AFFX-r2-Bs-thr_avg-signal162.191910
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal812.586487
Spike_AFFX-r2-Bs-phe_5_signal49.732529
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1326.520874
RawQ2.353377
Spike_AFFX-r2-Bs-lys_5_signal39.001701
Signal(A)5.282250
%A36.023674
Signal(All)147.327042
Corner+Avg:111,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal308.247589
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal123.799103
Spike_AFFX-r2-Ec-bioD_avg-signal1069.553711
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.928978
Spike_AFFX-r2-Bs-lys_avg-signal37.322620
Spike_AFFX-r2-P1-cre_avg-signal4318.050293
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.047348
Spike_AFFX-r2-Bs-thr_3_signal295.378174
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-signal75.455086
Spike_AFFX-r2-Bs-dap_3_signal506.493927
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.632467
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal286.798615
#M467
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal50.577915
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.074788
Spike_AFFX-r2-Bs-thr_M_signal134.896255
Signal(P)234.187485
Spike_AFFX-r2-Bs-phe_3-5-ratio2.489298
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8166,Count:9
Spike_AFFX-r2-P1-cre_5_signal3648.670654
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8217
Signal(M)19.257273
BackgroundAvg:78.68,Std:0.91,Min:76.7,Max:80.8
Spike_AFFX-r2-Ec-bioC_avg-signal297.523102
Spike_AFFX-r2-Bs-dap_avg-signal354.410492
Spike_AFFX-r2-Bs-dap_3-5-ratio3.056872
Spike_AFFX-r2-Ec-bioB_5_signal65.963249
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.760294
NF1.000000
HZ4
Tau0.015000

Slide: Arana_587-9_della-9hrs_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Arana_587-9_della-9hrs_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Arana_587-9_della-9hrs_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: della
Stock Code: N16298
Genetic Background: Ler(Landsberg_erecta)
Age: 5 days old
Growth Conditions:
StratificationSeeds were stratified for 4 days in MS (Murashige & Skoog medium) including modified vitamins, Duchefa Biuochemie.
SterilisationSurface- sterilized with 10 min in 1 ml ethanol 70% Triton 0,05% followed by 7 min in ETOH 96%.
ProtocolSeedlings were grown under photoperiodic conditions; 8h white light, 16 h darkness. Light intensity: 200 µE. Continuous temperature: 22 °C, 50% humidity for 5 days. Medium: MS with modified vitamins.
Percentage Agrose8
Substrate Sterilising Procedureautoclave 20 min
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent. Intensity: 200µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: transposon insertion
Tissue: whole plant
Additional Organism Information:
Sample Description5 days old whole seedlings
Other Information:
Timecourse start procedureTime 0 is the moment in which the lights are on, and the “day” starts.

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:0.98297
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-ratio1.215664
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.360480
Spike_AFFX-r2-Bs-dap_5_signal908.813477
NoiseAvg:1.89,Std:0.05,Min:1.8,Max:2.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal301.018066
#P14029
Spike_AFFX-r2-Bs-phe_M_signal304.997711
Corner-Avg:12544,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal191.992889
Spike_AFFX-r2-Ec-bioB_3_signal177.576553
Spike_AFFX-r2-Bs-lys_M_signal145.147095
Spike_AFFX-r2-P1-cre_3_signal8412.202148
Spike_AFFX-r2-Bs-lys_3-5-ratio1.252626
Spike_AFFX-r2-Bs-dap_M_signal1705.752197
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.436586
Spike_AFFX-r2-Ec-bioB_avg-signal166.698135
Spike_AFFX-r2-Bs-thr_avg-signal798.552673
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1806.238770
Spike_AFFX-r2-Bs-phe_5_signal281.136292
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2791.433105
RawQ1.956241
Spike_AFFX-r2-Bs-lys_5_signal190.450134
Signal(A)5.368842
%A36.624287
Signal(All)156.898453
Corner+Avg:98,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal581.473450
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal600.857239
Spike_AFFX-r2-Ec-bioD_avg-signal2298.835938
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.503727
Spike_AFFX-r2-Bs-lys_avg-signal191.386673
Spike_AFFX-r2-P1-cre_avg-signal7666.022949
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.871986
Spike_AFFX-r2-Bs-thr_3_signal1335.492676
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-signal395.663727
Spike_AFFX-r2-Bs-dap_3_signal2236.250488
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.545440
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal543.470581
#M427
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal238.562820
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.069926
Spike_AFFX-r2-Bs-thr_M_signal759.147278
Signal(P)251.318069
Spike_AFFX-r2-Bs-phe_3-5-ratio2.137245
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10254,Count:9
Spike_AFFX-r2-P1-cre_5_signal6919.843750
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8354
Signal(M)19.347040
BackgroundAvg:68.90,Std:0.40,Min:67.6,Max:69.7
Spike_AFFX-r2-Ec-bioC_avg-signal562.472046
Spike_AFFX-r2-Bs-dap_avg-signal1616.938843
Spike_AFFX-r2-Bs-dap_3-5-ratio2.460626
Spike_AFFX-r2-Ec-bioB_5_signal130.524948
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.982970
NF1.000000
HZ4
Tau0.015000

Slide: Arana_587-10_della-21hrs_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 ("Arana_587-10_della-21hrs_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: Arana_587-10_della-21hrs_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: della
Stock Code: N16298
Genetic Background: Ler(Landsberg_erecta)
Age: 5 days old
Growth Conditions:
StratificationSeeds were stratified for 4 days in MS (Murashige & Skoog medium) including modified vitamins, Duchefa Biuochemie.
SterilisationSurface- sterilized with 10 min in 1 ml ethanol 70% Triton 0,05% followed by 7 min in ETOH 96%.
ProtocolSeedlings were grown under photoperiodic conditions; 8h white light, 16 h darkness. Light intensity: 200 µE. Continuous temperature: 22 °C, 50% humidity for 5 days. Medium: MS with modified vitamins.
Percentage Agrose8
Substrate Sterilising Procedureautoclave 20 min
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent. Intensity: 200µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: transposon insertion
Tissue: whole plant
Additional Organism Information:
Sample Description5 days old whole seedlings
Other Information:
Timecourse start procedureTime 0 is the moment in which the lights are on, and the “day” starts.

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:1.040391
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-ratio1.209359
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.549239
Spike_AFFX-r2-Bs-dap_5_signal314.438721
NoiseAvg:2.45,Std:0.09,Min:2.2,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal128.645279
#P13013
Spike_AFFX-r2-Bs-phe_M_signal113.541245
Corner-Avg:9560,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal119.356064
Spike_AFFX-r2-Ec-bioB_3_signal100.881149
Spike_AFFX-r2-Bs-lys_M_signal55.140369
Spike_AFFX-r2-P1-cre_3_signal6004.895020
Spike_AFFX-r2-Bs-lys_3-5-ratio1.408820
Spike_AFFX-r2-Bs-dap_M_signal611.618164
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.646425
Spike_AFFX-r2-Ec-bioB_avg-signal95.117928
Spike_AFFX-r2-Bs-thr_avg-signal347.969849
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1074.933594
Spike_AFFX-r2-Bs-phe_5_signal89.011757
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1847.127930
RawQ2.398727
Spike_AFFX-r2-Bs-lys_5_signal90.078636
Signal(A)6.407275
%A40.832970
Signal(All)152.148163
Corner+Avg:84,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal387.193756
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal165.595886
Spike_AFFX-r2-Ec-bioD_avg-signal1461.030762
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.049541
Spike_AFFX-r2-Bs-lys_avg-signal90.707855
Spike_AFFX-r2-P1-cre_avg-signal5485.124512
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.117492
Spike_AFFX-r2-Bs-thr_3_signal597.740662
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-signal122.716301
Spike_AFFX-r2-Bs-dap_3_signal749.736145
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.718365
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal366.204285
#M483
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal126.904549
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.057316
Spike_AFFX-r2-Bs-thr_M_signal317.523590
Signal(P)261.284576
Spike_AFFX-r2-Bs-phe_3-5-ratio1.860382
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6974,Count:9
Spike_AFFX-r2-P1-cre_5_signal4965.354004
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9314
Signal(M)22.207260
BackgroundAvg:54.71,Std:1.25,Min:52.5,Max:58.6
Spike_AFFX-r2-Ec-bioC_avg-signal376.699036
Spike_AFFX-r2-Bs-dap_avg-signal558.597656
Spike_AFFX-r2-Bs-dap_3-5-ratio2.384363
Spike_AFFX-r2-Ec-bioB_5_signal65.116577
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.040391
NF1.000000
HZ4
Tau0.015000

Slide: Arana_587-11_della-21hrs_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 ("Arana_587-11_della-21hrs_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: Arana_587-11_della-21hrs_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: della
Stock Code: N16298
Genetic Background: Ler(Landsberg_erecta)
Age: 5 days old
Growth Conditions:
StratificationSeeds were stratified for 4 days in MS (Murashige & Skoog medium) including modified vitamins, Duchefa Biuochemie.
SterilisationSurface- sterilized with 10 min in 1 ml ethanol 70% Triton 0,05% followed by 7 min in ETOH 96%.
ProtocolSeedlings were grown under photoperiodic conditions; 8h white light, 16 h darkness. Light intensity: 200 µE. Continuous temperature: 22 °C, 50% humidity for 5 days. Medium: MS with modified vitamins.
Percentage Agrose8
Substrate Sterilising Procedureautoclave 20 min
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent. Intensity: 200µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: transposon insertion
Tissue: whole plant
Additional Organism Information:
Sample Description5 days old whole seedlings
Other Information:
Timecourse start procedureTime 0 is the moment in which the lights are on, and the “day” starts.

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:0.84009
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-ratio1.148123
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.426247
Spike_AFFX-r2-Bs-dap_5_signal249.801468
NoiseAvg:2.18,Std:0.09,Min:2.0,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal83.805618
#P13814
Spike_AFFX-r2-Bs-phe_M_signal87.356598
Corner-Avg:13216,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal151.397430
Spike_AFFX-r2-Ec-bioB_3_signal146.077179
Spike_AFFX-r2-Bs-lys_M_signal43.714813
Spike_AFFX-r2-P1-cre_3_signal6392.031250
Spike_AFFX-r2-Bs-lys_3-5-ratio1.811664
Spike_AFFX-r2-Bs-dap_M_signal531.115112
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.142490
Spike_AFFX-r2-Ec-bioB_avg-signal133.298431
Spike_AFFX-r2-Bs-thr_avg-signal252.345596
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1376.354126
Spike_AFFX-r2-Bs-phe_5_signal75.737152
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2253.397949
RawQ2.025750
Spike_AFFX-r2-Bs-lys_5_signal51.809834
Signal(A)5.256824
%A37.400265
Signal(All)155.363312
Corner+Avg:107,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal507.712402
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal135.834732
Spike_AFFX-r2-Ec-bioD_avg-signal1814.875977
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.561157
Spike_AFFX-r2-Bs-lys_avg-signal63.128880
Spike_AFFX-r2-P1-cre_avg-signal5979.703613
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.038579
Spike_AFFX-r2-Bs-thr_3_signal430.969574
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-signal99.642822
Spike_AFFX-r2-Bs-dap_3_signal794.989868
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.637223
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal450.876312
#M465
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal93.861992
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.126057
Spike_AFFX-r2-Bs-thr_M_signal242.261597
Signal(P)252.624481
Spike_AFFX-r2-Bs-phe_3-5-ratio1.793502
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9979,Count:9
Spike_AFFX-r2-P1-cre_5_signal5567.375977
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8531
Signal(M)19.864042
BackgroundAvg:50.31,Std:0.41,Min:49.5,Max:51.4
Spike_AFFX-r2-Ec-bioC_avg-signal479.294373
Spike_AFFX-r2-Bs-dap_avg-signal525.302185
Spike_AFFX-r2-Bs-dap_3-5-ratio3.182487
Spike_AFFX-r2-Ec-bioB_5_signal102.420677
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.840090
NF1.000000
HZ4
Tau0.015000

Slide: Arana_587-12_della-21hrs_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Arana_587-12_della-21hrs_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Arana_587-12_della-21hrs_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: della
Stock Code: N16298
Genetic Background: Ler(Landsberg_erecta)
Age: 5 days old
Growth Conditions:
StratificationSeeds were stratified for 4 days in MS (Murashige & Skoog medium) including modified vitamins, Duchefa Biuochemie.
SterilisationSurface- sterilized with 10 min in 1 ml ethanol 70% Triton 0,05% followed by 7 min in ETOH 96%.
ProtocolSeedlings were grown under photoperiodic conditions; 8h white light, 16 h darkness. Light intensity: 200 µE. Continuous temperature: 22 °C, 50% humidity for 5 days. Medium: MS with modified vitamins.
Percentage Agrose8
Substrate Sterilising Procedureautoclave 20 min
Temperature22 °C average, 22 °C day, 22 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Fluorescent. Intensity: 200µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: transposon insertion
Tissue: whole plant
Additional Organism Information:
Sample Description5 days old whole seedlings
Other Information:
Timecourse start procedureTime 0 is the moment in which the lights are on, and the “day” starts.

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:0.766792
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-ratio1.271566
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.598965
Spike_AFFX-r2-Bs-dap_5_signal368.360565
NoiseAvg:2.12,Std:0.05,Min:1.9,Max:2.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal123.555153
#P14102
Spike_AFFX-r2-Bs-phe_M_signal116.765320
Corner-Avg:13874,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal204.204544
Spike_AFFX-r2-Ec-bioB_3_signal162.053345
Spike_AFFX-r2-Bs-lys_M_signal56.540562
Spike_AFFX-r2-P1-cre_3_signal8059.645020
Spike_AFFX-r2-Bs-lys_3-5-ratio1.633513
Spike_AFFX-r2-Bs-dap_M_signal739.519409
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.270730
Spike_AFFX-r2-Ec-bioB_avg-signal155.868942
Spike_AFFX-r2-Bs-thr_avg-signal267.106476
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1966.342041
Spike_AFFX-r2-Bs-phe_5_signal107.532799
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2737.365723
RawQ2.116796
Spike_AFFX-r2-Bs-lys_5_signal70.691116
Signal(A)4.466449
%A36.225338
Signal(All)156.807816
Corner+Avg:133,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal617.033997
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal180.379044
Spike_AFFX-r2-Ec-bioD_avg-signal2351.854004
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.823761
Spike_AFFX-r2-Bs-lys_avg-signal80.902176
Spike_AFFX-r2-P1-cre_avg-signal7199.003418
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.950899
Spike_AFFX-r2-Bs-thr_3_signal404.115479
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal134.892380
Spike_AFFX-r2-Bs-dap_3_signal1061.907715
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.392111
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal565.084412
#M445
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal115.474846
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.091932
Spike_AFFX-r2-Bs-thr_M_signal273.648834
Signal(P)250.501190
Spike_AFFX-r2-Bs-phe_3-5-ratio1.677433
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10835,Count:9
Spike_AFFX-r2-P1-cre_5_signal6338.361816
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8263
Signal(M)16.431866
BackgroundAvg:49.81,Std:0.39,Min:48.5,Max:50.6
Spike_AFFX-r2-Ec-bioC_avg-signal591.059204
Spike_AFFX-r2-Bs-dap_avg-signal723.262512
Spike_AFFX-r2-Bs-dap_3-5-ratio2.882794
Spike_AFFX-r2-Ec-bioB_5_signal101.348930
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.766792
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team