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Experiment: Modulation of AMP1 expression and activity

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-652

To assess the transcriptomic effect of AMP1 overexpression we generated an estradiol-inducible AMP1 overexpression construct (ESR>>AMP1:MYC; Zuo et al., 2000) and brought it into the amp1-1 background. AMP1 encodes a putative glutamate carboxypeptidase and its loss of function results in increased shoot meristem activity. To identify short-time responses to increased AMP1 expression we induced ESR>>AMP1:MYC for 6h and 24h, respectively, and compared it to the DMSO treated mock control. We also included as control 6h DMSO-treated Col-0 and 6h DMSO-treated amp1-13 samples.In parallel we treated Col-0 plants for 6h, 24h and 10 days with chemical 32C8 which induces amp1-like phenotypes in wild-type and compared it tomock-treated wild-type and amp1-13 plants.Plants were grown under long-day conditions at 22°C and whole seedlings were used for RNA extraction.Zuo, J., Niu, Q. W.,&Chua, N. H. (2000) 24: 265-273

About the Experimenter

Name:Dr Tobias Sieberer
Head of Lab Name:Dr Tobias Sieberer
Lab:
Address:Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna
Dr. Bohrgasse 9/4, Wien, Vienna, 1030, AUSTRIA
Postcode: 1030
Country: AUSTRIA
 

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

About this Experiment

Experiment Type: compound_based_treatment
Number of Slides:11
 
Experimental Parameters:
parametergenetic_modification
Quality Control Measures Taken:
References:
Reference Zuo J, Niu QW, Chua NH. An estrogen receptor-based transactivator XVE mediates highly inducible gene expression in transgenic plants. Plant J. 2000;24:265-273
 
Other Information:

Slides in this Experiment

Hybridisation Set: Sieberer: Modulation of AMP1 expression and activity

Slide: Sieberer_652-1_WT+DMSO_6h_ATH1

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

Summary Information

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

  • Extract 1 ("Sieberer_652-1_WT+DMSO_6h_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: Sieberer_652-1_WT+DMSO_6h_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code: N70000
Genetic Background: Col-0 (Columbia)
Growth Conditions:
StratificationPlate the seeds on agar medium. Seal the Petri dish. Put in dark at +40C for 2 days.
Sterilisation1. Put Arabidopsis seeds in epi-tube. 2. Add 70% ethanol + 0,5 mg/ml SDS. Keep for 3 min. inverting the tube. Discard the supernatant. 3. Add 96% ethanol for 1min. Discard the supernatant. 4. Leave seeds in open epi-tube for drying under the sterile conditions.
ProtocolAfter stratification procedure plates with seeds are moved to the plant growth room. Plants were grown for 9 days at long-day conditions. At 9th day the whole seedlings were taken out of agar and placed into a liquid growth medium (the same medium just without agar) and incubated in such conditions for 1 day. At the next day (10th day) dimethyl sulfoxide (10µl DMSO/1ml of liquid medium) for 6 hours was added. After the DMSO treatment seedlings were frozen in liquid nitrogen and transferred to -80C.
Percentage Agrose0,8
Substrate Sterilising ProcedureAutoclavation: Time: 20 min. Temperature: 121 oC Pressure: 1 bar
Temperature22 °C average, 24 °C day, 20 °C night
Humidity50 % average, 50 % day, 50 % night
MediumOwn medium: For 1litre ATS medium, use 5 ml 1M KNO3 2,5 ml 1M KH2PO4 buffer (adjusted to pH 5.5) 2 ml 1M MgSO4 2 ml 1M Ca(NO3)2 2.5 ml 20mM Fe-EDTA 1 ml micronutrients 10g sucrose 8g agar Micronutrients stock solution (1 litre) 70 mM H3BO3 14 mM MnCl2 0,5 mM CuSO4 1 mM ZnSO4 0,2 mM NaMoO4 10 mM NaCl 0,01 mM CoCl2
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: ecotype
Tissue: whole plant
in vivo Treatment: At 9th day the whole seedlings were taken out of agar medium and placed into a liquid growth medium (the same medium just without agar) and incubated in such conditions for 1 day. At the next day (10th day) dimethyl sulfoxide (10µl DMSO/1ml of liquid medium) for 6 hours was added. After the DMSO treatment seedlings were frozen in liquid nitrogen and transferred to -80C.
Additional Organism Information:
Sample DescriptionHealthy plant
Other Information:
Timecourse start procedure

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:0.468829
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-ratio1.317884
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.980121
Spike_AFFX-r2-Bs-dap_5_signal33.730095
NoiseAvg:3.05,Std:0.09,Min:2.8,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.601931
#P15011
Spike_AFFX-r2-Bs-phe_M_signal16.472492
Corner-Avg:8332,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal58.703045
Spike_AFFX-r2-Ec-bioB_3_signal41.898064
Spike_AFFX-r2-Bs-lys_M_signal13.319605
Spike_AFFX-r2-P1-cre_3_signal3370.762451
Spike_AFFX-r2-Bs-lys_3-5-ratio2.045593
Spike_AFFX-r2-Bs-dap_M_signal117.346573
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.413110
Spike_AFFX-r2-Ec-bioB_avg-signal47.782986
Spike_AFFX-r2-Bs-thr_avg-signal42.158966
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal511.153381
Spike_AFFX-r2-Bs-phe_5_signal10.635600
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal717.875244
RawQ2.715172
Spike_AFFX-r2-Bs-lys_5_signal17.658094
Signal(A)3.781386
%A32.569050
Signal(All)140.327011
Corner+Avg:151,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal193.842484
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal38.114517
Spike_AFFX-r2-Ec-bioD_avg-signal614.514282
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.808853
Spike_AFFX-r2-Bs-lys_avg-signal22.366325
Spike_AFFX-r2-P1-cre_avg-signal2964.234863
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.622096
Spike_AFFX-r2-Bs-thr_3_signal86.761665
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal21.740870
Spike_AFFX-r2-Bs-dap_3_signal249.737106
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.404422
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal175.617477
#M370
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal36.121277
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.103777
Spike_AFFX-r2-Bs-thr_M_signal32.113308
Signal(P)211.000748
Spike_AFFX-r2-Bs-phe_3-5-ratio3.583673
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7014,Count:9
Spike_AFFX-r2-P1-cre_5_signal2557.707031
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7429
Signal(M)14.688789
BackgroundAvg:71.81,Std:1.27,Min:68.5,Max:74.9
Spike_AFFX-r2-Ec-bioC_avg-signal184.729980
Spike_AFFX-r2-Bs-dap_avg-signal133.604599
Spike_AFFX-r2-Bs-dap_3-5-ratio7.403985
Spike_AFFX-r2-Ec-bioB_5_signal42.747849
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.468829
NF1.000000
HZ4
Tau0.015000

Slide: Sieberer_652-2_WT+DMSO_const_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 ("Sieberer_652-2_WT+DMSO_const_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: Sieberer_652-2_WT+DMSO_const_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code: N70000
Genetic Background: Col-0 (Columbia)
Growth Conditions:
StratificationUnder the sterile conditions. Add 100 µl of liquid MS medium, DMSO (final concentration 10 µl/ml) to the 96 multi well plate. Distribute the seeds into a 96 multi well plate, approximately 5 seeds per well. Seal the plate. Put in the dark to +40C for 2 days.
Sterilisation1. Put Arabidopsis seeds in epi-tube. 2. Add 70% ethanol + 0,5 mg/ml SDS. Keep for 3 min. inverting the tube. Discard the supernatant. 3. Add 96% ethanol for 1min. Discard the supernatant. 4. Leave seeds in open epi-tube for drying under the sterile conditions.
ProtocolAfter stratification procedure plates with seeds are moved to the plant growth room. Plants were grown for 10 days at long-day conditions. Then seedlings were frozen in liquid nitrogen and transferred to -80C.
Substrate Sterilising ProcedureAutoclavation: Time: 20 min. Temperature: 121 oC Pressure: 1 bar
Temperature22 °C average, 24 °C day, 20 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture. Modifications: For 1litre MS medium, use MS powder MES 0,5g Sucrose 10g pH 5.7
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: ecotype
Tissue: whole plant
in vivo Treatment: DMSO control treatment 10 µl/ml
Additional Organism Information:
Sample DescriptionHealthy plant
Other Information:
Timecourse start procedure

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:0.619333
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-ratio1.175651
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.908981
Spike_AFFX-r2-Bs-dap_5_signal19.592125
NoiseAvg:2.98,Std:0.08,Min:2.7,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.906580
#P15133
Spike_AFFX-r2-Bs-phe_M_signal11.779716
Corner-Avg:7458,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal66.715179
Spike_AFFX-r2-Ec-bioB_3_signal45.493572
Spike_AFFX-r2-Bs-lys_M_signal6.712661
Spike_AFFX-r2-P1-cre_3_signal3121.267578
Spike_AFFX-r2-Bs-lys_3-5-ratio2.523948
Spike_AFFX-r2-Bs-dap_M_signal60.840153
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.990215
Spike_AFFX-r2-Ec-bioB_avg-signal54.085911
Spike_AFFX-r2-Bs-thr_avg-signal26.467428
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal478.109741
Spike_AFFX-r2-Bs-phe_5_signal12.320515
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal799.661804
RawQ2.831608
Spike_AFFX-r2-Bs-lys_5_signal7.697632
Signal(A)3.899390
%A31.985971
Signal(All)137.514221
Corner+Avg:131,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal198.431503
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.888372
Spike_AFFX-r2-Ec-bioD_avg-signal638.885742
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P66.343712
Spike_AFFX-r2-Bs-lys_avg-signal11.279572
Spike_AFFX-r2-P1-cre_avg-signal2888.097656
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.670320
Spike_AFFX-r2-Bs-thr_3_signal47.509815
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal15.662868
Spike_AFFX-r2-Bs-dap_3_signal130.397720
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.672549
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal167.730225
#M381
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal19.428425
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.183040
Spike_AFFX-r2-Bs-thr_M_signal19.985889
Signal(P)205.004272
Spike_AFFX-r2-Bs-phe_3-5-ratio1.857745
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6053,Count:9
Spike_AFFX-r2-P1-cre_5_signal2654.927734
Spike_AFFX-r2-Bs-phe_M_detectionM
#A7296
Signal(M)15.537090
BackgroundAvg:70.55,Std:0.44,Min:68.8,Max:71.3
Spike_AFFX-r2-Ec-bioC_avg-signal183.080872
Spike_AFFX-r2-Bs-dap_avg-signal70.276665
Spike_AFFX-r2-Bs-dap_3-5-ratio6.655619
Spike_AFFX-r2-Ec-bioB_5_signal50.048985
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.619333
NF1.000000
HZ4
Tau0.015000

Slide: Sieberer_652-3_Line1+DMSO_6h_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 ("Sieberer_652-3_Line1+DMSO_6h_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: Sieberer_652-3_Line1+DMSO_6h_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
StratificationPlate the seeds on agar medium. Seal the Petri dish. Put in dark at +40C for 2 days.
Sterilisation1. Put Arabidopsis seeds in epi-tube. 2. Add 70% ethanol + 0,5 mg/ml SDS. Keep for 3 min. inverting the tube. Discard the supernatant. 3. Add 96% ethanol for 1min. Discard the supernatant. 4. Leave seeds in open epi-tube for drying under the sterile conditions.
ProtocolAfter stratification procedure plates with seeds are moved to the plant growth room. Plants were grown for 9 days at long-day conditions. At 9th day the whole seedlings were taken out of agar and placed into a liquid growth medium (the same medium just without agar) and incubated in such conditions for 1 day. At the next day (10th day) dimethyl sulfoxide (10µl DMSO/1ml of liquid medium) for 6 hours was added. After the DMSO treatment seedlings were frozen in liquid nitrogen and transferred to -80C.
Percentage Agrose0,8
Substrate Sterilising ProcedureAutoclavation: Time: 20 min. Temperature: 121 oC Pressure: 1 bar
Temperature22 °C average, 24 °C day, 20 °C night
Humidity50 % average, 50 % day, 50 % night
MediumOwn medium: For 1litre ATS medium, use 5 ml 1M KNO3 2,5 ml 1M KH2PO4 buffer (adjusted to pH 5.5) 2 ml 1M MgSO4 2 ml 1M Ca(NO3)2 2.5 ml 20mM Fe-EDTA 1 ml micronutrients 10g sucrose 8g agar Micronutrients stock solution (1 litre) 70 mM H3BO3 14 mM MnCl2 0,5 mM CuSO4 1 mM ZnSO4 0,2 mM NaMoO4 10 mM NaCl 0,01 mM CoCl2
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in Line 1 represents amp1-1(N8324) transformed with construct pER8-AMP1::6xMYC. pER8-AMP1::6xMYC was generated by cloning the AMP1 ORF (At3g54720) fused to a C-terminal 6xMYC-tag into vector pER8 (Zuo et al., 2000, The Plant Journal 24
Tissue: whole plant
in vivo Treatment: At 9th day the whole seedlings were taken out of agar medium and placed into a liquid growth medium (the same medium just without agar) and incubated in such conditions for 1 day. At the next day (10th day) dimethyl sulfoxide (10µl DMSO/1ml of liquid medium) for 6 hours was added. After the DMSO treatment seedlings were frozen in liquid nitrogen and transferred to -80C.
Additional Organism Information:
Sample DescriptionHealthy plant
Other Information:
Timecourse start procedure

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:0.631682
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-ratio1.141493
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.094181
Spike_AFFX-r2-Bs-dap_5_signal23.031914
NoiseAvg:2.71,Std:0.06,Min:2.5,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal2.157208
#P14649
Spike_AFFX-r2-Bs-phe_M_signal13.059740
Corner-Avg:7348,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal84.495392
Spike_AFFX-r2-Ec-bioB_3_signal54.637920
Spike_AFFX-r2-Bs-lys_M_signal10.005814
Spike_AFFX-r2-P1-cre_3_signal3634.778076
Spike_AFFX-r2-Bs-lys_3-5-ratio2.322738
Spike_AFFX-r2-Bs-dap_M_signal68.072594
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio28.426121
Spike_AFFX-r2-Ec-bioB_avg-signal63.022770
Spike_AFFX-r2-Bs-thr_avg-signal32.968575
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal574.206848
Spike_AFFX-r2-Bs-phe_5_signal8.685172
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal825.697144
RawQ2.537340
Spike_AFFX-r2-Bs-lys_5_signal8.258805
Signal(A)4.523755
%A34.028934
Signal(All)144.162399
Corner+Avg:128,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal224.508102
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal25.652042
Spike_AFFX-r2-Ec-bioD_avg-signal699.952026
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P64.221832
Spike_AFFX-r2-Bs-lys_avg-signal12.482553
Spike_AFFX-r2-P1-cre_avg-signal3409.505127
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.749233
Spike_AFFX-r2-Bs-thr_3_signal61.321060
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal15.798985
Spike_AFFX-r2-Bs-dap_3_signal153.845917
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.437979
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal229.246811
#M399
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal19.183039
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.979329
Spike_AFFX-r2-Bs-thr_M_signal35.427452
Signal(P)221.623718
Spike_AFFX-r2-Bs-phe_3-5-ratio2.953545
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6054,Count:9
Spike_AFFX-r2-P1-cre_5_signal3184.232178
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7762
Signal(M)16.704424
BackgroundAvg:66.49,Std:0.53,Min:64.4,Max:67.4
Spike_AFFX-r2-Ec-bioC_avg-signal226.877457
Spike_AFFX-r2-Bs-dap_avg-signal81.650146
Spike_AFFX-r2-Bs-dap_3-5-ratio6.679685
Spike_AFFX-r2-Ec-bioB_5_signal49.934994
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.631682
NF1.000000
HZ4
Tau0.015000

Slide: Sieberer_652-4_Line1+DMSO_24h_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 ("Sieberer_652-4_Line1+DMSO_24h_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: Sieberer_652-4_Line1+DMSO_24h_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
StratificationPlate the seeds on agar medium. Seal the Petri dish. Put in dark at +40C for 2 days.
Sterilisation1. Put Arabidopsis seeds in epi-tube. 2. Add 70% ethanol + 0,5 mg/ml SDS. Keep for 3 min. inverting the tube. Discard the supernatant. 3. Add 96% ethanol for 1min. Discard the supernatant. 4. Leave seeds in open epi-tube for drying under the sterile conditions.
ProtocolAfter stratification procedure plates with seeds are moved to the plant growth room. Plants were grown for 9 days at long-day conditions. At 9th day the whole seedlings were taken out of agar and placed into a liquid growth medium (the same medium just without agar) and incubated in such conditions for 1 day. At the next day (10th day) dimethyl sulfoxide (10µl DMSO/1ml of liquid medium) for 24 hours was added. After the DMSO treatment seedlings were frozen in liquid nitrogen and transferred to -80C.
Percentage Agrose0,8
Substrate Sterilising ProcedureAutoclavation: Time: 20 min. Temperature: 121 oC Pressure: 1 bar
Temperature22 °C average, 24 °C day, 20 °C night
Humidity50 % average, 50 % day, 50 % night
MediumOwn medium: For 1litre ATS medium, use 5 ml 1M KNO3 2,5 ml 1M KH2PO4 buffer (adjusted to pH 5.5) 2 ml 1M MgSO4 2 ml 1M Ca(NO3)2 2.5 ml 20mM Fe-EDTA 1 ml micronutrients 10g sucrose 8g agar Micronutrients stock solution (1 litre) 70 mM H3BO3 14 mM MnCl2 0,5 mM CuSO4 1 mM ZnSO4 0,2 mM NaMoO4 10 mM NaCl 0,01 mM CoCl2
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in Line 1 represents amp1-1(N8324) transformed with construct pER8-AMP1::6xMYC. pER8-AMP1::6xMYC was generated by cloning the AMP1 ORF (At3g54720) fused to a C-terminal 6xMYC-tag into vector pER8 (Zuo et al., 2000, The Plant Journal 24
Tissue: whole plant
in vivo Treatment: At 9th day the whole seedlings were taken out of agar medium and placed into a liquid growth medium (the same medium just without agar) and incubated in such conditions for 1 day. At the next day (10th day) dimethyl sulfoxide (10µl DMSO/1ml of liquid medium) for 24 hours was added. After the DMSO treatment seedlings were frozen in liquid nitrogen and transferred to -80C.
Additional Organism Information:
Sample DescriptionHealthy plant
Other Information:
Timecourse start procedure

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:0.591848
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-ratio1.320874
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.411688
Spike_AFFX-r2-Bs-dap_5_signal39.866997
NoiseAvg:2.88,Std:0.09,Min:2.6,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.085715
#P14706
Spike_AFFX-r2-Bs-phe_M_signal21.942402
Corner-Avg:7750,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal70.094299
Spike_AFFX-r2-Ec-bioB_3_signal51.700249
Spike_AFFX-r2-Bs-lys_M_signal10.168257
Spike_AFFX-r2-P1-cre_3_signal3779.895752
Spike_AFFX-r2-Bs-lys_3-5-ratio3.697784
Spike_AFFX-r2-Bs-dap_M_signal107.722305
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.501009
Spike_AFFX-r2-Ec-bioB_avg-signal52.805847
Spike_AFFX-r2-Bs-thr_avg-signal52.978359
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal547.179077
Spike_AFFX-r2-Bs-phe_5_signal20.864185
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal755.839722
RawQ2.636210
Spike_AFFX-r2-Bs-lys_5_signal11.212707
Signal(A)4.676494
%A33.704517
Signal(All)144.214691
Corner+Avg:138,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal200.968658
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal34.860771
Spike_AFFX-r2-Ec-bioD_avg-signal651.509399
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.471725
Spike_AFFX-r2-Bs-lys_avg-signal20.947710
Spike_AFFX-r2-P1-cre_avg-signal3320.778809
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.823761
Spike_AFFX-r2-Bs-thr_3_signal105.325478
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-signal25.889120
Spike_AFFX-r2-Bs-dap_3_signal231.933136
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.381339
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal178.337250
#M416
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal41.462170
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.126902
Spike_AFFX-r2-Bs-thr_M_signal42.523891
Signal(P)220.729599
Spike_AFFX-r2-Bs-phe_3-5-ratio1.670843
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6434,Count:9
Spike_AFFX-r2-P1-cre_5_signal2861.662109
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7688
Signal(M)18.112492
BackgroundAvg:68.69,Std:0.66,Min:66.9,Max:69.8
Spike_AFFX-r2-Ec-bioC_avg-signal189.652954
Spike_AFFX-r2-Bs-dap_avg-signal126.507484
Spike_AFFX-r2-Bs-dap_3-5-ratio5.817673
Spike_AFFX-r2-Ec-bioB_5_signal36.622997
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.591848
NF1.000000
HZ4
Tau0.015000

Slide: Sieberer_652-5_Line1+ES_6h_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 ("Sieberer_652-5_Line1+ES_6h_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: Sieberer_652-5_Line1+ES_6h_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
StratificationPlate the seeds on agar medium. Seal the Petri dish. Put in dark at +40C for 2 days.
Sterilisation1. Put Arabidopsis seeds in epi-tube. 2. Add 70% ethanol + 0,5 mg/ml SDS. Keep for 3 min. inverting the tube. Discard the supernatant. 3. Add 96% ethanol for 1min. Discard the supernatant. 4. Leave seeds in open epi-tube for drying under the sterile conditions.
ProtocolAfter stratification procedure plates with seeds are moved to the plant growth room. Plants were grown for 9 days at long-day conditions. At 9th day the whole seedlings were taken out of agar and placed into a liquid growth medium (the same medium just without agar) and incubated in such conditions for 1 day. At the next day (10th day) estradiol (50µM) for 6 hours was added. After the estradiol treatment seedlings were frozen in liquid nitrogen and transferred to -80C.
Percentage Agrose0,8
Substrate Sterilising ProcedureAutoclavation: Time: 20 min. Temperature: 121 oC Pressure: 1 bar
Temperature22 °C average, 24 °C day, 20 °C night
Humidity50 % average, 50 % day, 50 % night
MediumOwn medium: For 1litre ATS medium, use 5 ml 1M KNO3 2,5 ml 1M KH2PO4 buffer (adjusted to pH 5.5) 2 ml 1M MgSO4 2 ml 1M Ca(NO3)2 2.5 ml 20mM Fe-EDTA 1 ml micronutrients 10g sucrose 8g agar Micronutrients stock solution (1 litre) 70 mM H3BO3 14 mM MnCl2 0,5 mM CuSO4 1 mM ZnSO4 0,2 mM NaMoO4 10 mM NaCl 0,01 mM CoCl2
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in Line 1 represents amp1-1(N8324) transformed with construct pER8-AMP1::6xMYC. pER8-AMP1::6xMYC was generated by cloning the AMP1 ORF (At3g54720) fused to a C-terminal 6xMYC-tag into vector pER8 (Zuo et al., 2000, The Plant Journal 24
Tissue: whole plant
in vivo Treatment: At 9th day the whole seedlings were taken out of agar and placed into a liquid growth medium (the same medium just without agar) and incubated in such conditions for 1 day. At the next day (10th day) estradiol (50µM) for 6 hours was added. After the estradiol treatment seedlings were frozen in liquid nitrogen and transferred to -80C.
Additional Organism Information:
Sample DescriptionHealthy plant
Other Information:
Timecourse start procedure

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:0.698215
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-ratio1.438500
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.902836
Spike_AFFX-r2-Bs-dap_5_signal11.802290
NoiseAvg:2.41,Std:0.06,Min:2.3,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.205769
#P14647
Spike_AFFX-r2-Bs-phe_M_signal5.373960
Corner-Avg:5769,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal81.432724
Spike_AFFX-r2-Ec-bioB_3_signal67.471169
Spike_AFFX-r2-Bs-lys_M_signal3.325311
Spike_AFFX-r2-P1-cre_3_signal5035.380371
Spike_AFFX-r2-Bs-lys_3-5-ratio3.593444
Spike_AFFX-r2-Bs-dap_M_signal43.410027
Spike_AFFX-r2-Bs-thr_M_detectionM
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.657116
Spike_AFFX-r2-Ec-bioB_avg-signal74.545448
Spike_AFFX-r2-Bs-thr_avg-signal25.586975
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal690.202576
Spike_AFFX-r2-Bs-phe_5_signal0.730693
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal893.578003
RawQ2.395716
Spike_AFFX-r2-Bs-lys_5_signal5.895611
Signal(A)4.010613
%A34.050854
Signal(All)145.867447
Corner+Avg:99,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal312.568573
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.091452
Spike_AFFX-r2-Ec-bioD_avg-signal791.890259
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P64.213066
Spike_AFFX-r2-Bs-lys_avg-signal10.135490
Spike_AFFX-r2-P1-cre_avg-signal4267.908691
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.736081
Spike_AFFX-r2-Bs-thr_3_signal46.420982
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal9.065368
Spike_AFFX-r2-Bs-dap_3_signal100.769028
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.294660
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal278.666138
#M396
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.185549
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.121660
Spike_AFFX-r2-Bs-thr_M_signal22.134182
Signal(P)224.600037
Spike_AFFX-r2-Bs-phe_3-5-ratio21.091452
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4823,Count:9
Spike_AFFX-r2-P1-cre_5_signal3500.437256
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7767
Signal(M)16.084160
BackgroundAvg:61.33,Std:0.42,Min:60.1,Max:62.5
Spike_AFFX-r2-Ec-bioC_avg-signal295.617371
Spike_AFFX-r2-Bs-dap_avg-signal51.993778
Spike_AFFX-r2-Bs-dap_3-5-ratio8.538091
Spike_AFFX-r2-Ec-bioB_5_signal74.732437
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.698215
NF1.000000
HZ4
Tau0.015000

Slide: Sieberer_652-6_Line1+ES_24h_ATH1

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

Summary Information

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

  • Extract 1 ("Sieberer_652-6_Line1+ES_24h_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: Sieberer_652-6_Line1+ES_24h_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code:
Growth Conditions:
StratificationPlate the seeds on agar medium. Seal the Petri dish. Put in dark at +40C for 2 days.
Sterilisation1. Put Arabidopsis seeds in epi-tube. 2. Add 70% ethanol + 0,5 mg/ml SDS. Keep for 3 min. inverting the tube. Discard the supernatant. 3. Add 96% ethanol for 1min. Discard the supernatant. 4. Leave seeds in open epi-tube for drying under the sterile conditions.
ProtocolAfter stratification procedure plates with seeds are moved to the plant growth room. Plants were grown for 9 days at long-day conditions. At 9th day the whole seedlings were taken out of agar and placed into a liquid growth medium (the same medium just without agar) and incubated in such conditions for 1 day. At the next day (10th day) estradiol (50µM) for 24 hours was added. After the estradiol treatment seedlings were frozen in liquid nitrogen and transferred to -80C.
Percentage Agrose0,8
Substrate Sterilising ProcedureAutoclavation: Time: 20 min. Temperature: 121 oC Pressure: 1 bar
Temperature22 °C average, 24 °C day, 20 °C night
Humidity50 % average, 50 % day, 50 % night
MediumOwn medium: For 1litre ATS medium, use 5 ml 1M KNO3 2,5 ml 1M KH2PO4 buffer (adjusted to pH 5.5) 2 ml 1M MgSO4 2 ml 1M Ca(NO3)2 2.5 ml 20mM Fe-EDTA 1 ml micronutrients 10g sucrose 8g agar Micronutrients stock solution (1 litre) 70 mM H3BO3 14 mM MnCl2 0,5 mM CuSO4 1 mM ZnSO4 0,2 mM NaMoO4 10 mM NaCl 0,01 mM CoCl2
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: knock out mutation in Line 1 represents amp1-1(N8324) transformed with construct pER8-AMP1::6xMYC. pER8-AMP1::6xMYC was generated by cloning the AMP1 ORF (At3g54720) fused to a C-terminal 6xMYC-tag into vector pER8 (Zuo et al., 2000, The Plant Journal 24
Tissue: whole plant
in vivo Treatment: At 9th day the whole seedlings were taken out of agar and placed into a liquid growth medium (the same medium just without agar) and incubated in such conditions for 1 day. At the next day (10th day) estradiol (50µM) for 24 hours was added. After the estradiol treatment seedlings were frozen in liquid nitrogen and transferred to -80C.
Additional Organism Information:
Sample DescriptionHealthy plant
Other Information:
Timecourse start procedure

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:1.441502
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-ratio1.040706
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.127883
Spike_AFFX-r2-Bs-dap_5_signal27.094950
NoiseAvg:2.14,Std:0.22,Min:1.3,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_signal4.857576
#P13406
Spike_AFFX-r2-Bs-phe_M_signal8.917865
Corner-Avg:5250,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal88.254433
Spike_AFFX-r2-Ec-bioB_3_signal89.830399
Spike_AFFX-r2-Bs-lys_M_signal10.737883
Spike_AFFX-r2-P1-cre_3_signal5089.982910
Spike_AFFX-r2-Bs-lys_3-5-ratio1.916899
Spike_AFFX-r2-Bs-dap_M_signal25.379213
Spike_AFFX-r2-Bs-thr_M_detectionM
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio19.416729
Spike_AFFX-r2-Ec-bioB_avg-signal85.909996
Spike_AFFX-r2-Bs-thr_avg-signal47.870831
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal966.673157
Spike_AFFX-r2-Bs-phe_5_signal1.881489
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1528.223267
RawQ1.750878
Spike_AFFX-r2-Bs-lys_5_signal7.960970
Signal(A)6.263781
%A39.193336
Signal(All)154.277451
Corner+Avg:139,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal584.918518
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal32.762417
Spike_AFFX-r2-Ec-bioD_avg-signal1247.448242
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P58.772469
Spike_AFFX-r2-Bs-lys_avg-signal11.319743
Spike_AFFX-r2-P1-cre_avg-signal4990.439453
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.034195
Spike_AFFX-r2-Bs-thr_3_signal94.318237
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-signal14.520591
Spike_AFFX-r2-Bs-dap_3_signal158.622421
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.580910
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal431.052673
#M464
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal15.260373
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.356954
Spike_AFFX-r2-Bs-thr_M_signal44.436676
Signal(P)257.514648
Spike_AFFX-r2-Bs-phe_3-5-ratio17.413027
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:2682,Count:9
Spike_AFFX-r2-P1-cre_5_signal4890.896484
Spike_AFFX-r2-Bs-phe_M_detectionM
#A8940
Signal(M)23.339159
BackgroundAvg:43.75,Std:2.39,Min:38.7,Max:50.3
Spike_AFFX-r2-Ec-bioC_avg-signal507.985596
Spike_AFFX-r2-Bs-dap_avg-signal70.365532
Spike_AFFX-r2-Bs-dap_3-5-ratio5.854317
Spike_AFFX-r2-Ec-bioB_5_signal79.645142
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.441502
NF1.000000
HZ4
Tau0.015000

Slide: Sieberer_652-7_amp1.13+DMSO_6h_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 ("Sieberer_652-7_amp1.13+DMSO_6h_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: Sieberer_652-7_amp1.13+DMSO_6h_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_022988 (AZ)
Stock Code: N522988
Genetic Background: Col-0 (Columbia, N60000)
Growth Conditions:
StratificationPlate the seeds on agar medium. Seal the Petri dish. Put in dark at +40C for 2 days.
Sterilisation1. Put Arabidopsis seeds in epi-tube. 2. Add 70% ethanol + 0,5 mg/ml SDS. Keep for 3 min. inverting the tube. Discard the supernatant. 3. Add 96% ethanol for 1min. Discard the supernatant. 4. Leave seeds in open epi-tube for drying under the sterile conditions.
ProtocolAfter stratification procedure plates with seeds are moved to the plant growth room. Plants were grown for 9 days at long-day conditions (16 h light/8 h dark; light intensity 140 umol/m2/s). At 9th day the whole seedlings were taken out of agar and placed into a liquid growth medium (the same medium just without agar) and incubated in such conditions for 1 day. At the next day (10th day) dimethyl sulfoxide (10µl DMSO/1ml of liquid medium) for 6 hours was added. After the DMSO treatment seedlings were frozen in liquid nitrogen and transferred to -80C.
Percentage Agrose0,8
Substrate Sterilising ProcedureAutoclavation: Time: 20 min. Temperature: 121 oC Pressure: 1 bar
Temperature22 °C average, 24 °C day, 20 °C night
Humidity50 % average, 50 % day, 50 % night
MediumOwn medium: For 1litre ATS medium, use 5 ml 1M KNO3 2,5 ml 1M KH2PO4 buffer (adjusted to pH 5.5) 2 ml 1M MgSO4 2 ml 1M Ca(NO3)2 2.5 ml 20mM Fe-EDTA 1 ml micronutrients 10g sucrose 8g agar Micronutrients stock solution (1 litre) 70 mM H3BO3 14 mM MnCl2 0,5 mM CuSO4 1 mM ZnSO4 0,2 mM NaMoO4 10 mM NaCl 0,01 mM CoCl2
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA Insertion
Tissue: whole plant
in vivo Treatment: At 9th day the whole seedlings were taken out of agar medium and placed into a liquid growth medium (the same medium just without agar) and incubated in such conditions for 1 day. At the next day (10th day) dimethyl sulfoxide (10µl DMSO/1ml of liquid medium) for 6 hours was added. After the DMSO treatment seedlings were frozen in liquid nitrogen and transferred to -80C.
Additional Organism Information:
Sample DescriptionHealthy plant
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.725518
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-ratio1.379207
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.084474
Spike_AFFX-r2-Bs-dap_5_signal18.632988
NoiseAvg:2.35,Std:0.06,Min:2.2,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.581480
#P14720
Spike_AFFX-r2-Bs-phe_M_signal12.010534
Corner-Avg:6048,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal85.438553
Spike_AFFX-r2-Ec-bioB_3_signal77.269173
Spike_AFFX-r2-Bs-lys_M_signal11.699111
Spike_AFFX-r2-P1-cre_3_signal5145.394043
Spike_AFFX-r2-Bs-lys_3-5-ratio2.329873
Spike_AFFX-r2-Bs-dap_M_signal70.358177
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.668689
Spike_AFFX-r2-Ec-bioB_avg-signal77.986031
Spike_AFFX-r2-Bs-thr_avg-signal25.867577
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal769.033264
Spike_AFFX-r2-Bs-phe_5_signal13.673478
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal921.896301
RawQ2.327128
Spike_AFFX-r2-Bs-lys_5_signal10.699452
Signal(A)4.087160
%A33.866726
Signal(All)143.096100
Corner+Avg:123,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal320.315643
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal18.908037
Spike_AFFX-r2-Ec-bioD_avg-signal845.464783
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.533096
Spike_AFFX-r2-Bs-lys_avg-signal15.775643
Spike_AFFX-r2-P1-cre_avg-signal4438.042480
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.600175
Spike_AFFX-r2-Bs-thr_3_signal50.558529
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-signal14.864017
Spike_AFFX-r2-Bs-dap_3_signal167.484772
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.198773
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal283.201050
#M365
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.928370
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.131054
Spike_AFFX-r2-Bs-thr_M_signal19.462719
Signal(P)219.196991
Spike_AFFX-r2-Bs-phe_3-5-ratio1.382826
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5000,Count:9
Spike_AFFX-r2-P1-cre_5_signal3730.691162
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7725
Signal(M)16.079811
BackgroundAvg:58.11,Std:0.53,Min:57.0,Max:59.7
Spike_AFFX-r2-Ec-bioC_avg-signal301.758362
Spike_AFFX-r2-Bs-dap_avg-signal85.491982
Spike_AFFX-r2-Bs-dap_3-5-ratio8.988616
Spike_AFFX-r2-Ec-bioB_5_signal71.250374
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.725518
NF1.000000
HZ4
Tau0.015000

Slide: Sieberer_652-8_amp1.13+DMSO_const_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 ("Sieberer_652-8_amp1.13+DMSO_const_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: Sieberer_652-8_amp1.13+DMSO_const_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_022988 (AZ)
Stock Code: N522988
Genetic Background: Col-0 (Columbia, N60000)
Growth Conditions:
StratificationUnder sterile conditions. Add 100 µl of liquid MS medium, DMSO (final concentration 10 µl/ml) to a 96 multi well plate. Distribute the seeds into a 96 multi well plate, approximately 5 seeds per well. Seal the plate. Put in the dark to +40C for 2 days.
Sterilisation1. Put Arabidopsis seeds in epi-tube. 2. Add 70% ethanol + 0,5 mg/ml SDS. Keep for 3 min. inverting the tube. Discard the supernatant. 3. Add 96% ethanol for 1min. Discard the supernatant. 4. Leave seeds in open epi-tube for drying under the sterile conditions.
ProtocolAfter stratification procedure plates with seeds are moved to the plant growth room. Plants were grown for 10 days at long-day conditions. Then seedlings were frozen in liquid nitrogen and transferred to -80C.
Substrate Sterilising ProcedureAutoclavation: Time: 20 min. Temperature: 121 oC Pressure: 1 bar
Temperature22 °C average, 24 °C day, 20 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture. Modifications: For 1litre MS medium, use MS powder MES 0,5g Sucrose 10g pH 5.7
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA Insertion
Tissue: whole plant
in vivo Treatment: DMSO control treatment (10µl/ml)
Additional Organism Information:
Sample DescriptionHealthy plant
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.124329
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-ratio1.285656
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.801730
Spike_AFFX-r2-Bs-dap_5_signal10.853881
NoiseAvg:1.90,Std:0.05,Min:1.7,Max:2.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.249158
#P14374
Spike_AFFX-r2-Bs-phe_M_signal7.665299
Corner-Avg:5072,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal81.057320
Spike_AFFX-r2-Ec-bioB_3_signal73.820274
Spike_AFFX-r2-Bs-lys_M_signal9.764638
Spike_AFFX-r2-P1-cre_3_signal4861.783203
Spike_AFFX-r2-Bs-lys_3-5-ratio2.169414
Spike_AFFX-r2-Bs-dap_M_signal61.567364
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.294984
Spike_AFFX-r2-Ec-bioB_avg-signal82.317955
Spike_AFFX-r2-Bs-thr_avg-signal39.027969
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal724.869080
Spike_AFFX-r2-Bs-phe_5_signal13.347350
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal881.001770
RawQ2.024549
Spike_AFFX-r2-Bs-lys_5_signal11.581119
Signal(A)4.986386
%A35.120560
Signal(All)142.601486
Corner+Avg:84,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal343.235229
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.089348
Spike_AFFX-r2-Ec-bioD_avg-signal802.935425
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P63.016220
Spike_AFFX-r2-Bs-lys_avg-signal15.490001
Spike_AFFX-r2-P1-cre_avg-signal4321.670410
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.863218
Spike_AFFX-r2-Bs-thr_3_signal77.108253
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionM
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal14.033999
Spike_AFFX-r2-Bs-dap_3_signal166.208435
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.215394
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal275.467163
#M425
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal25.124243
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.246011
Spike_AFFX-r2-Bs-thr_M_signal27.726490
Signal(P)222.988419
Spike_AFFX-r2-Bs-phe_3-5-ratio1.580040
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4223,Count:9
Spike_AFFX-r2-P1-cre_5_signal3781.557617
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8011
Signal(M)17.784472
BackgroundAvg:52.36,Std:0.26,Min:51.8,Max:53.1
Spike_AFFX-r2-Ec-bioC_avg-signal309.351196
Spike_AFFX-r2-Bs-dap_avg-signal79.543228
Spike_AFFX-r2-Bs-dap_3-5-ratio15.313272
Spike_AFFX-r2-Ec-bioB_5_signal92.076279
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.124329
NF1.000000
HZ4
Tau0.015000

Slide: Sieberer_652-9_WT+32_C8_6h_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 ("Sieberer_652-9_WT+32_C8_6h_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: Sieberer_652-9_WT+32_C8_6h_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code: N70000
Genetic Background: Col-0 (Columbia)
Growth Conditions:
StratificationPlate the seeds on agar medium. Seal the Petri dish. Put in dark at +40C for 2 days.
Sterilisation1. Put Arabidopsis seeds in epi-tube. 2. Add 70% ethanol + 0,5 mg/ml SDS. Keep for 3 min. inverting the tube. Discard the supernatant. 3. Add 96% ethanol for 1min. Discard the supernatant. 4. Leave seeds in open epi-tube for drying under the sterile conditions.
ProtocolAfter stratification procedure plates with seeds are moved to the plant growth room. Plants were grown for 9 days at long-day conditions. At 9th day the whole seedlings were taken out of agar and placed into a liquid growth medium (the same medium just without agar) and incubated in such conditions for 1 day. At the next day (10th day) chemical called 32C8 (50 µM) for 6 hours was added. After the 32C8 treatment seedlings were frozen in liquid nitrogen and transferred to -80C.
Percentage Agrose0,8
Substrate Sterilising ProcedureAutoclavation: Time: 20 min. Temperature: 121 oC Pressure: 1 bar
Temperature22 °C average, 24 °C day, 20 °C night
Humidity50 % average, 50 % day, 50 % night
MediumOwn medium: For 1litre ATS medium, use 5 ml 1M KNO3 2,5 ml 1M KH2PO4 buffer (adjusted to pH 5.5) 2 ml 1M MgSO4 2 ml 1M Ca(NO3)2 2.5 ml 20mM Fe-EDTA 1 ml micronutrients 10g sucrose 8g agar Micronutrients stock solution (1 litre) 70 mM H3BO3 14 mM MnCl2 0,5 mM CuSO4 1 mM ZnSO4 0,2 mM NaMoO4 10 mM NaCl 0,01 mM CoCl2
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: ecotype
Tissue: whole plant
in vivo Treatment: At 9th day the whole seedlings were taken out of agar and placed into a liquid growth medium (the same medium just without agar) and incubated in such conditions for 1 day. At the next day (10th day) chemical 32C8 (50 µM) for 6 hours was added. After the 32C8 treatment seedlings were frozen in liquid nitrogen and transferred to -80C.
Additional Organism Information:
Sample DescriptionHealthy plant
Other Information:
Timecourse start procedure

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:1.151675
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-ratio1.162056
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.079178
Spike_AFFX-r2-Bs-dap_5_signal14.930101
NoiseAvg:2.04,Std:0.09,Min:1.8,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_signal1.179862
#P14031
Spike_AFFX-r2-Bs-phe_M_signal10.274110
Corner-Avg:4799,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal95.607826
Spike_AFFX-r2-Ec-bioB_3_signal95.890717
Spike_AFFX-r2-Bs-lys_M_signal7.293277
Spike_AFFX-r2-P1-cre_3_signal5181.964844
Spike_AFFX-r2-Bs-lys_3-5-ratio3.521611
Spike_AFFX-r2-Bs-dap_M_signal50.028530
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio38.077824
Spike_AFFX-r2-Ec-bioB_avg-signal93.451271
Spike_AFFX-r2-Bs-thr_avg-signal28.005470
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal944.563171
Spike_AFFX-r2-Bs-phe_5_signal5.163026
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1197.065308
RawQ2.140731
Spike_AFFX-r2-Bs-lys_5_signal5.296803
Signal(A)5.037832
%A36.483997
Signal(All)147.592606
Corner+Avg:92,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal438.388855
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal14.424300
Spike_AFFX-r2-Ec-bioD_avg-signal1070.814209
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P61.512493
Spike_AFFX-r2-Bs-lys_avg-signal10.414453
Spike_AFFX-r2-P1-cre_avg-signal4820.636230
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.003507
Spike_AFFX-r2-Bs-thr_3_signal44.926563
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal9.953812
Spike_AFFX-r2-Bs-dap_3_signal131.494308
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.267322
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal419.255737
#M457
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal18.653280
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.045636
Spike_AFFX-r2-Bs-thr_M_signal37.909985
Signal(P)236.346268
Spike_AFFX-r2-Bs-phe_3-5-ratio2.793769
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:3773,Count:9
Spike_AFFX-r2-P1-cre_5_signal4459.307617
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8322
Signal(M)18.573441
BackgroundAvg:53.44,Std:0.21,Min:52.8,Max:54.1
Spike_AFFX-r2-Ec-bioC_avg-signal428.822296
Spike_AFFX-r2-Bs-dap_avg-signal65.484314
Spike_AFFX-r2-Bs-dap_3-5-ratio8.807328
Spike_AFFX-r2-Ec-bioB_5_signal88.855293
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.151675
NF1.000000
HZ4
Tau0.015000

Slide: Sieberer_652-10_WT+32_C8_24h_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 ("Sieberer_652-10_WT+32_C8_24h_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: Sieberer_652-10_WT+32_C8_24h_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code: N70000
Genetic Background: Col-0 (Columbia)
Growth Conditions:
StratificationPlate the seeds on agar medium. Seal the Petri dish. Put in dark at +40C for 2 days.
Sterilisation1. Put Arabidopsis seeds in epi-tube. 2. Add 70% ethanol + 0,5 mg/ml SDS. Keep for 3 min. inverting the tube. Discard the supernatant. 3. Add 96% ethanol for 1min. Discard the supernatant. 4. Leave seeds in open epi-tube for drying under the sterile conditions.
ProtocolAfter stratification procedure plates with seeds are moved to the plant growth room. Plants were grown for 9 days at long-day conditions. At 9th day the whole seedlings were taken out of agar and placed into a liquid growth medium (the same medium just without agar) and incubated in such conditions for 1 day. At the next day (10th day) chemical called 32C8 (50 µM) for 24 hours was added. After the 32C8 treatment seedlings were frozen in liquid nitrogen and transferred to -80C.
Percentage Agrose0,8
Substrate Sterilising ProcedureAutoclavation: Time: 20 min. Temperature: 121 oC Pressure: 1 bar
Temperature22 °C average, 24 °C day, 20 °C night
Humidity50 % average, 50 % day, 50 % night
MediumOwn medium: For 1litre ATS medium, use 5 ml 1M KNO3 2,5 ml 1M KH2PO4 buffer (adjusted to pH 5.5) 2 ml 1M MgSO4 2 ml 1M Ca(NO3)2 2.5 ml 20mM Fe-EDTA 1 ml micronutrients 10g sucrose 8g agar Micronutrients stock solution (1 litre) 70 mM H3BO3 14 mM MnCl2 0,5 mM CuSO4 1 mM ZnSO4 0,2 mM NaMoO4 10 mM NaCl 0,01 mM CoCl2
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: ecotype
Tissue: whole plant
in vivo Treatment: At 9th day the whole seedlings were taken out of agar and placed into a liquid growth medium (the same medium just without agar) and incubated in such conditions for 1 day. At the next day (10th day) chemical 32C8 (50 µM) for 24 hours was added. After the 32C8 treatment seedlings were frozen in liquid nitrogen and transferred to -80C.
Additional Organism Information:
Sample DescriptionHealthy plant
Other Information:
Timecourse start procedure

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:0.720002
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-ratio1.455718
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.900258
Spike_AFFX-r2-Bs-dap_5_signal18.574993
NoiseAvg:2.59,Std:0.10,Min:2.4,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal11.867422
#P14423
Spike_AFFX-r2-Bs-phe_M_signal8.199567
Corner-Avg:6082,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal88.097130
Spike_AFFX-r2-Ec-bioB_3_signal67.703964
Spike_AFFX-r2-Bs-lys_M_signal14.207428
Spike_AFFX-r2-P1-cre_3_signal5002.464355
Spike_AFFX-r2-Bs-lys_3-5-ratio3.716036
Spike_AFFX-r2-Bs-dap_M_signal49.278465
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.824763
Spike_AFFX-r2-Ec-bioB_avg-signal77.002068
Spike_AFFX-r2-Bs-thr_avg-signal34.518150
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal728.239868
Spike_AFFX-r2-Bs-phe_5_signal5.699657
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal926.660217
RawQ2.510901
Spike_AFFX-r2-Bs-lys_5_signal6.527197
Signal(A)4.450528
%A34.940815
Signal(All)145.494232
Corner+Avg:108,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal344.107941
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal14.504941
Spike_AFFX-r2-Ec-bioD_avg-signal827.450073
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P63.231037
Spike_AFFX-r2-Bs-lys_avg-signal14.996640
Spike_AFFX-r2-P1-cre_avg-signal4219.444336
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.828146
Spike_AFFX-r2-Bs-thr_3_signal57.257504
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal9.468055
Spike_AFFX-r2-Bs-dap_3_signal129.521561
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.272466
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal287.526428
#M417
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal24.255299
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.196787
Spike_AFFX-r2-Bs-thr_M_signal34.429523
Signal(P)227.142700
Spike_AFFX-r2-Bs-phe_3-5-ratio2.544879
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4551,Count:9
Spike_AFFX-r2-P1-cre_5_signal3436.424072
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7970
Signal(M)17.202942
BackgroundAvg:61.49,Std:0.38,Min:60.7,Max:62.6
Spike_AFFX-r2-Ec-bioC_avg-signal315.817200
Spike_AFFX-r2-Bs-dap_avg-signal65.791672
Spike_AFFX-r2-Bs-dap_3-5-ratio6.972899
Spike_AFFX-r2-Ec-bioB_5_signal75.205101
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.720002
NF1.000000
HZ4
Tau0.015000

Slide: Sieberer_652-11_WT+32_C8_const_ATH1

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

Summary Information

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

  • Extract 1 ("Sieberer_652-11_WT+32_C8_const_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: Sieberer_652-11_WT+32_C8_const_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0
Stock Code: N70000
Genetic Background: Col-0 (Columbia)
Growth Conditions:
StratificationUnder the sterile conditions. Add 100 µl of liquid MS medium, compound 32C8 (final concentration 50 µM) to the 96 multi well plate. Distribute the seeds into a 96 multi well plate, approximately 5 seeds per well. Seal the plate. Put in the dark to +40C for 2 days.
Sterilisation1. Put Arabidopsis seeds in epi-tube. 2. Add 70% ethanol + 0,5 mg/ml SDS. Keep for 3 min. inverting the tube. Discard the supernatant. 3. Add 96% ethanol for 1min. Discard the supernatant. 4. Leave seeds in open epi-tube for drying under the sterile conditions.
ProtocolAfter stratification procedure plates with seeds are moved to the plant growth room. Plants were grown for 10 days at long-day conditions. Then seedlings were frozen in liquid nitrogen and transferred to -80C.
Substrate Sterilising ProcedureAutoclavation: Time: 20 min. Temperature: 121 oC Pressure: 1 bar
Temperature22 °C average, 24 °C day, 20 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige & Skoog basal salt mixture. Modifications: For 1litre MS medium, use MS powder MES 0,5g Sucrose 10g pH 5.7
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: ecotype
Tissue: whole plant
in vivo Treatment: chemical 32C8 50µM
Additional Organism Information:
Sample DescriptionHealthy plant
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.62901
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-ratio1.470388
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.691370
Spike_AFFX-r2-Bs-dap_5_signal18.417006
NoiseAvg:2.66,Std:0.09,Min:2.5,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.653898
#P14939
Spike_AFFX-r2-Bs-phe_M_signal13.944251
Corner-Avg:6617,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal87.029572
Spike_AFFX-r2-Ec-bioB_3_signal71.012939
Spike_AFFX-r2-Bs-lys_M_signal8.409674
Spike_AFFX-r2-P1-cre_3_signal4729.221191
Spike_AFFX-r2-Bs-lys_3-5-ratio2.273493
Spike_AFFX-r2-Bs-dap_M_signal54.922009
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.661396
Spike_AFFX-r2-Ec-bioB_avg-signal66.675987
Spike_AFFX-r2-Bs-thr_avg-signal31.346640
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal770.424072
Spike_AFFX-r2-Bs-phe_5_signal11.188749
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal963.111572
RawQ2.509077
Spike_AFFX-r2-Bs-lys_5_signal9.039086
Signal(A)3.881550
%A32.906620
Signal(All)139.357971
Corner+Avg:116,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal325.872040
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal13.864768
Spike_AFFX-r2-Ec-bioD_avg-signal866.767822
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.493202
Spike_AFFX-r2-Bs-lys_avg-signal12.666351
Spike_AFFX-r2-P1-cre_avg-signal3972.764648
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.600175
Spike_AFFX-r2-Bs-thr_3_signal65.932343
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal12.999256
Spike_AFFX-r2-Bs-dap_3_signal151.424118
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.250106
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal293.120422
#M365
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal20.550295
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.111734
Spike_AFFX-r2-Bs-thr_M_signal22.453674
Signal(P)210.469818
Spike_AFFX-r2-Bs-phe_3-5-ratio1.239171
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5155,Count:9
Spike_AFFX-r2-P1-cre_5_signal3216.307861
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7506
Signal(M)14.826887
BackgroundAvg:62.32,Std:0.67,Min:61.1,Max:63.8
Spike_AFFX-r2-Ec-bioC_avg-signal309.496216
Spike_AFFX-r2-Bs-dap_avg-signal74.921043
Spike_AFFX-r2-Bs-dap_3-5-ratio8.221972
Spike_AFFX-r2-Ec-bioB_5_signal41.985451
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.629010
NF1.000000
HZ4
Tau0.015000


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