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Experiment: Long recovery after heat shock

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-562

Abiotic stress is a major factor for crop productivity, a problem likely to be exacerbated by climate change. Improving the tolerance to environmental stress is one of the most important goals of crop breeding programmes. While the early responses to abiotic stress in plants are well studied, plant adaptation to enduring or recurring stress conditions has received little attention. This project investigates the molecular mechanism of the maintenance of acquired thermotolerance as a model case of stress memory in Arabidopsis. Arabidopsis seedlings acquire thermotolerance through a heat treatment at sublethal temperatures. To investigate the underlying mechanisms, we are investigating changes in the transcriptome at two timepoints after a heat acclimation treatment using Arabidopsis thaliana seedlings.

About the Experimenter

Name: Isabel Baurle
Head of Lab Name: Isabel Baurle
Lab:
Address:Department of Disease and Stress Biology, John Innes Centre
Norwich Research Park, Colney Lane, Norwich, Norfolk, NR4 7UH, UNITED KINGDOM
Postcode:
Country:
 
Telephone Number: 01603-450328
Fax Number: 01603-450025

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: stimulus_or_stress_design
Number of Slides:27
 
Experimental Parameters:
parameterchange_temperature
parametertimepoint
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Baurle: long recovery after heat shock

Slide: Baurle_562-1_Col_contr_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("Baurle_562-1_Col_contr_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-1_Col_contr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-4 (Columbia)
Stock Code: N933
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample Descriptionwhole 3d old seedling
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:0.474854
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-ratio1.343072
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.180748
Spike_AFFX-r2-Bs-dap_5_signal82.524765
NoiseAvg:2.59,Std:0.05,Min:2.5,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_signal22.866596
#P15137
Spike_AFFX-r2-Bs-phe_M_signal20.132313
Corner-Avg:10299,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal68.663689
Spike_AFFX-r2-Ec-bioB_3_signal67.971405
Spike_AFFX-r2-Bs-lys_M_signal12.582558
Spike_AFFX-r2-P1-cre_3_signal4301.114258
Spike_AFFX-r2-Bs-lys_3-5-ratio2.238667
Spike_AFFX-r2-Bs-dap_M_signal125.471283
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.804968
Spike_AFFX-r2-Ec-bioB_avg-signal64.733833
Spike_AFFX-r2-Bs-thr_avg-signal34.732990
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal730.499390
Spike_AFFX-r2-Bs-phe_5_signal16.653540
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1002.219482
RawQ2.401191
Spike_AFFX-r2-Bs-lys_5_signal14.743369
Signal(A)3.690286
%A32.029812
Signal(All)146.947342
Corner+Avg:157,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal228.963089
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal31.089550
Spike_AFFX-r2-Ec-bioD_avg-signal866.359436
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.361244
Spike_AFFX-r2-Bs-lys_avg-signal20.110472
Spike_AFFX-r2-P1-cre_avg-signal3751.779297
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.608943
Spike_AFFX-r2-Bs-thr_3_signal41.273472
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-signal22.625135
Spike_AFFX-r2-Bs-dap_3_signal183.291367
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.371965
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal200.288406
#M367
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal33.005489
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.143167
Spike_AFFX-r2-Bs-thr_M_signal40.058903
Signal(P)219.299042
Spike_AFFX-r2-Bs-phe_3-5-ratio1.866843
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7924,Count:9
Spike_AFFX-r2-P1-cre_5_signal3202.444092
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7306
Signal(M)14.654313
BackgroundAvg:52.66,Std:0.35,Min:51.9,Max:54.0
Spike_AFFX-r2-Ec-bioC_avg-signal214.625748
Spike_AFFX-r2-Bs-dap_avg-signal130.429138
Spike_AFFX-r2-Bs-dap_3-5-ratio2.221047
Spike_AFFX-r2-Ec-bioB_5_signal57.566406
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.474854
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-2_Col_contr_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Baurle_562-2_Col_contr_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-2_Col_contr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-4 (Columbia)
Stock Code: N933
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample Descriptionwhole 3d old seedling
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:0.643379
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-ratio1.381217
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.049873
Spike_AFFX-r2-Bs-dap_5_signal92.294403
NoiseAvg:2.51,Std:0.08,Min:2.3,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal32.343361
#P14736
Spike_AFFX-r2-Bs-phe_M_signal23.204731
Corner-Avg:9945,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal125.620461
Spike_AFFX-r2-Ec-bioB_3_signal88.350868
Spike_AFFX-r2-Bs-lys_M_signal9.775360
Spike_AFFX-r2-P1-cre_3_signal5499.496094
Spike_AFFX-r2-Bs-lys_3-5-ratio0.969408
Spike_AFFX-r2-Bs-dap_M_signal179.168808
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.673212
Spike_AFFX-r2-Ec-bioB_avg-signal99.375061
Spike_AFFX-r2-Bs-thr_avg-signal57.200714
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal767.253540
Spike_AFFX-r2-Bs-phe_5_signal26.950439
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1363.548584
RawQ2.480445
Spike_AFFX-r2-Bs-lys_5_signal25.641142
Signal(A)4.074618
%A33.722054
Signal(All)149.820404
Corner+Avg:154,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal265.303864
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal46.520111
Spike_AFFX-r2-Ec-bioD_avg-signal1065.401123
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.603241
Spike_AFFX-r2-Bs-lys_avg-signal20.091074
Spike_AFFX-r2-P1-cre_avg-signal4740.563965
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.674704
Spike_AFFX-r2-Bs-thr_3_signal86.460655
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-signal32.225094
Spike_AFFX-r2-Bs-dap_3_signal163.932770
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.777181
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal266.765594
#M382
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.856720
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.994521
Spike_AFFX-r2-Bs-thr_M_signal52.798138
Signal(P)229.381699
Spike_AFFX-r2-Bs-phe_3-5-ratio1.726135
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6887,Count:9
Spike_AFFX-r2-P1-cre_5_signal3981.632080
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7692
Signal(M)15.426161
BackgroundAvg:58.39,Std:0.77,Min:55.9,Max:60.4
Spike_AFFX-r2-Ec-bioC_avg-signal266.034729
Spike_AFFX-r2-Bs-dap_avg-signal145.131989
Spike_AFFX-r2-Bs-dap_3-5-ratio1.776194
Spike_AFFX-r2-Ec-bioB_5_signal84.153839
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.643379
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-3_Col_contr_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-3_Col_contr_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-3_Col_contr_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-4 (Columbia)
Stock Code: N933
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Additional Organism Information:
Sample Descriptionwhole 3d old seedling
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:0.554847
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.855672
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.149303
Spike_AFFX-r2-Bs-dap_5_signal60.339546
NoiseAvg:2.60,Std:0.08,Min:2.3,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal21.733252
#P15036
Spike_AFFX-r2-Bs-phe_M_signal20.417915
Corner-Avg:8939,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal88.914345
Spike_AFFX-r2-Ec-bioB_3_signal68.197220
Spike_AFFX-r2-Bs-lys_M_signal13.214698
Spike_AFFX-r2-P1-cre_3_signal3175.660889
Spike_AFFX-r2-Bs-lys_3-5-ratio2.900092
Spike_AFFX-r2-Bs-dap_M_signal150.430679
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.005782
Spike_AFFX-r2-Ec-bioB_avg-signal72.149826
Spike_AFFX-r2-Bs-thr_avg-signal45.598255
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal562.239990
Spike_AFFX-r2-Bs-phe_5_signal26.472786
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1148.757324
RawQ2.385113
Spike_AFFX-r2-Bs-lys_5_signal11.515690
Signal(A)3.934597
%A32.336693
Signal(All)147.015778
Corner+Avg:143,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal218.123871
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal33.180851
Spike_AFFX-r2-Ec-bioD_avg-signal855.498657
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.918457
Spike_AFFX-r2-Bs-lys_avg-signal19.375648
Spike_AFFX-r2-P1-cre_avg-signal3443.484375
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.744849
Spike_AFFX-r2-Bs-thr_3_signal65.325417
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-signal26.690516
Spike_AFFX-r2-Bs-dap_3_signal203.800247
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.043180
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal213.165817
#M398
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal33.396557
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.023259
Spike_AFFX-r2-Bs-thr_M_signal49.736099
Signal(P)220.690826
Spike_AFFX-r2-Bs-phe_3-5-ratio1.253395
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5207,Count:9
Spike_AFFX-r2-P1-cre_5_signal3711.307617
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7376
Signal(M)15.329610
BackgroundAvg:58.41,Std:0.38,Min:57.5,Max:59.4
Spike_AFFX-r2-Ec-bioC_avg-signal215.644836
Spike_AFFX-r2-Bs-dap_avg-signal138.190155
Spike_AFFX-r2-Bs-dap_3-5-ratio3.377557
Spike_AFFX-r2-Ec-bioB_5_signal59.337902
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.554847
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-4_Col_4h_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Baurle_562-4_Col_4h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-4_Col_4h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-4 (Columbia)
Stock Code: N933
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole 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:0.45358
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-ratio1.256991
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.051790
Spike_AFFX-r2-Bs-dap_5_signal107.856682
NoiseAvg:2.63,Std:0.10,Min:2.3,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal30.585348
#P15050
Spike_AFFX-r2-Bs-phe_M_signal35.919605
Corner-Avg:16363,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal90.560875
Spike_AFFX-r2-Ec-bioB_3_signal59.077618
Spike_AFFX-r2-Bs-lys_M_signal19.664255
Spike_AFFX-r2-P1-cre_3_signal4431.258301
Spike_AFFX-r2-Bs-lys_3-5-ratio1.857066
Spike_AFFX-r2-Bs-dap_M_signal205.176178
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.309013
Spike_AFFX-r2-Ec-bioB_avg-signal68.602379
Spike_AFFX-r2-Bs-thr_avg-signal61.898960
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal664.157959
Spike_AFFX-r2-Bs-phe_5_signal33.603199
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1174.369751
RawQ2.452034
Spike_AFFX-r2-Bs-lys_5_signal23.377151
Signal(A)3.250041
%A32.560280
Signal(All)143.193649
Corner+Avg:265,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal203.107224
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal50.348404
Spike_AFFX-r2-Ec-bioD_avg-signal919.263855
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.979836
Spike_AFFX-r2-Bs-lys_avg-signal28.818106
Spike_AFFX-r2-P1-cre_avg-signal3978.274414
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.459886
Spike_AFFX-r2-Bs-thr_3_signal101.207306
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-signal39.957066
Spike_AFFX-r2-Bs-dap_3_signal309.386627
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.768209
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal229.988983
#M333
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal43.412907
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.883117
Spike_AFFX-r2-Bs-thr_M_signal53.904232
Signal(P)215.142288
Spike_AFFX-r2-Bs-phe_3-5-ratio1.498322
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12470,Count:9
Spike_AFFX-r2-P1-cre_5_signal3525.290771
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7427
Signal(M)12.665083
BackgroundAvg:56.40,Std:0.46,Min:54.6,Max:57.8
Spike_AFFX-r2-Ec-bioC_avg-signal216.548096
Spike_AFFX-r2-Bs-dap_avg-signal207.473160
Spike_AFFX-r2-Bs-dap_3-5-ratio2.868498
Spike_AFFX-r2-Ec-bioB_5_signal56.168652
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.453580
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-5_Col_4h_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-5_Col_4h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-5_Col_4h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-4 (Columbia)
Stock Code: N933
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole 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:0.726184
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-ratio1.219439
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.363684
Spike_AFFX-r2-Bs-dap_5_signal104.265198
NoiseAvg:2.31,Std:0.10,Min:2.1,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_signal32.848801
#P14585
Spike_AFFX-r2-Bs-phe_M_signal30.180052
Corner-Avg:13865,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal102.642982
Spike_AFFX-r2-Ec-bioB_3_signal89.243385
Spike_AFFX-r2-Bs-lys_M_signal13.336400
Spike_AFFX-r2-P1-cre_3_signal4916.166016
Spike_AFFX-r2-Bs-lys_3-5-ratio1.826698
Spike_AFFX-r2-Bs-dap_M_signal201.934067
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.980004
Spike_AFFX-r2-Ec-bioB_avg-signal85.776405
Spike_AFFX-r2-Bs-thr_avg-signal68.766907
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal701.567017
Spike_AFFX-r2-Bs-phe_5_signal38.392914
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1264.001343
RawQ2.239988
Spike_AFFX-r2-Bs-lys_5_signal32.612049
Signal(A)4.368787
%A34.300747
Signal(All)144.205505
Corner+Avg:197,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal255.344910
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal64.935966
Spike_AFFX-r2-Ec-bioD_avg-signal982.784180
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.941254
Spike_AFFX-r2-Bs-lys_avg-signal35.173599
Spike_AFFX-r2-P1-cre_avg-signal4473.832031
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.758001
Spike_AFFX-r2-Bs-thr_3_signal97.889542
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-signal44.502979
Spike_AFFX-r2-Bs-dap_3_signal337.983307
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.801683
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal245.310455
#M401
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal59.572353
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.040905
Spike_AFFX-r2-Bs-thr_M_signal75.562378
Signal(P)222.768005
Spike_AFFX-r2-Bs-phe_3-5-ratio1.691353
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12250,Count:9
Spike_AFFX-r2-P1-cre_5_signal4031.498047
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7824
Signal(M)15.149194
BackgroundAvg:52.60,Std:0.54,Min:51.3,Max:54.0
Spike_AFFX-r2-Ec-bioC_avg-signal250.327682
Spike_AFFX-r2-Bs-dap_avg-signal214.727524
Spike_AFFX-r2-Bs-dap_3-5-ratio3.241574
Spike_AFFX-r2-Ec-bioB_5_signal65.442863
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.726184
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-6_Col_4h_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-6_Col_4h_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-6_Col_4h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-4 (Columbia)
Stock Code: N933
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole 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:0.520918
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-ratio1.233604
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.937001
Spike_AFFX-r2-Bs-dap_5_signal58.457806
NoiseAvg:2.53,Std:0.07,Min:2.3,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal24.377958
#P14941
Spike_AFFX-r2-Bs-phe_M_signal28.417933
Corner-Avg:9298,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal112.326309
Spike_AFFX-r2-Ec-bioB_3_signal55.858109
Spike_AFFX-r2-Bs-lys_M_signal19.455395
Spike_AFFX-r2-P1-cre_3_signal4711.401367
Spike_AFFX-r2-Bs-lys_3-5-ratio2.332930
Spike_AFFX-r2-Bs-dap_M_signal187.428650
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.417828
Spike_AFFX-r2-Ec-bioB_avg-signal75.932716
Spike_AFFX-r2-Bs-thr_avg-signal52.936779
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal718.690735
Spike_AFFX-r2-Bs-phe_5_signal28.662350
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1156.149902
RawQ2.476166
Spike_AFFX-r2-Bs-lys_5_signal16.524538
Signal(A)3.508049
%A32.775097
Signal(All)143.274368
Corner+Avg:147,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal243.677658
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal58.320900
Spike_AFFX-r2-Ec-bioD_avg-signal937.420288
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.501976
Spike_AFFX-r2-Bs-lys_avg-signal24.843508
Spike_AFFX-r2-P1-cre_avg-signal4265.309570
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.722929
Spike_AFFX-r2-Bs-thr_3_signal83.319672
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-signal38.467060
Spike_AFFX-r2-Bs-dap_3_signal239.806259
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.608689
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal252.609390
#M393
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal38.550591
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.964642
Spike_AFFX-r2-Bs-thr_M_signal51.112709
Signal(P)216.639236
Spike_AFFX-r2-Bs-phe_3-5-ratio2.034756
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7229,Count:9
Spike_AFFX-r2-P1-cre_5_signal3819.217285
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7476
Signal(M)12.863379
BackgroundAvg:56.19,Std:0.34,Min:55.0,Max:57.3
Spike_AFFX-r2-Ec-bioC_avg-signal248.143524
Spike_AFFX-r2-Bs-dap_avg-signal161.897568
Spike_AFFX-r2-Bs-dap_3-5-ratio4.102211
Spike_AFFX-r2-Ec-bioB_5_signal59.613743
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.520918
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-7_Col_52h_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("Baurle_562-7_Col_52h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-7_Col_52h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-4 (Columbia)
Stock Code: N933
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole 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:0.624491
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-ratio1.159068
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.232514
Spike_AFFX-r2-Bs-dap_5_signal93.566193
NoiseAvg:2.49,Std:0.06,Min:2.3,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.454411
#P14799
Spike_AFFX-r2-Bs-phe_M_signal35.365189
Corner-Avg:16048,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal82.146507
Spike_AFFX-r2-Ec-bioB_3_signal82.166283
Spike_AFFX-r2-Bs-lys_M_signal9.872779
Spike_AFFX-r2-P1-cre_3_signal4470.394043
Spike_AFFX-r2-Bs-lys_3-5-ratio1.951690
Spike_AFFX-r2-Bs-dap_M_signal163.094315
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.934821
Spike_AFFX-r2-Ec-bioB_avg-signal76.992790
Spike_AFFX-r2-Bs-thr_avg-signal52.205750
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal658.142395
Spike_AFFX-r2-Bs-phe_5_signal30.605286
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1360.025513
RawQ2.395733
Spike_AFFX-r2-Bs-lys_5_signal20.105339
Signal(A)3.967743
%A33.441475
Signal(All)146.184464
Corner+Avg:250,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal222.138351
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal36.897873
Spike_AFFX-r2-Ec-bioD_avg-signal1009.083984
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.879440
Spike_AFFX-r2-Bs-lys_avg-signal23.072500
Spike_AFFX-r2-P1-cre_avg-signal4163.640625
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.679088
Spike_AFFX-r2-Bs-thr_3_signal80.484436
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-signal34.289448
Spike_AFFX-r2-Bs-dap_3_signal178.387222
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.066461
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal226.535004
#M383
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal39.239384
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.980592
Spike_AFFX-r2-Bs-thr_M_signal55.678406
Signal(P)222.892365
Spike_AFFX-r2-Bs-phe_3-5-ratio1.205605
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12367,Count:9
Spike_AFFX-r2-P1-cre_5_signal3856.887451
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7628
Signal(M)14.667168
BackgroundAvg:55.32,Std:0.84,Min:53.2,Max:57.9
Spike_AFFX-r2-Ec-bioC_avg-signal224.336670
Spike_AFFX-r2-Bs-dap_avg-signal145.015915
Spike_AFFX-r2-Bs-dap_3-5-ratio1.906535
Spike_AFFX-r2-Ec-bioB_5_signal66.665581
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.624491
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-8_Col_52h_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-8_Col_52h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-8_Col_52h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-4 (Columbia)
Stock Code: N933
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole 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:0.494252
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-ratio1.242843
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.273770
Spike_AFFX-r2-Bs-dap_5_signal51.095341
NoiseAvg:2.49,Std:0.08,Min:2.3,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal19.996075
#P15111
Spike_AFFX-r2-Bs-phe_M_signal27.416334
Corner-Avg:8882,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal93.847916
Spike_AFFX-r2-Ec-bioB_3_signal80.463799
Spike_AFFX-r2-Bs-lys_M_signal9.279453
Spike_AFFX-r2-P1-cre_3_signal4494.051758
Spike_AFFX-r2-Bs-lys_3-5-ratio2.710980
Spike_AFFX-r2-Bs-dap_M_signal135.079666
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.327060
Spike_AFFX-r2-Ec-bioB_avg-signal79.160500
Spike_AFFX-r2-Bs-thr_avg-signal43.359863
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal653.407654
Spike_AFFX-r2-Bs-phe_5_signal22.176016
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1173.100098
RawQ2.410007
Spike_AFFX-r2-Bs-lys_5_signal12.401683
Signal(A)3.375314
%A32.091187
Signal(All)146.130814
Corner+Avg:133,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal238.133484
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal32.205666
Spike_AFFX-r2-Ec-bioD_avg-signal913.253906
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.247261
Spike_AFFX-r2-Bs-lys_avg-signal18.433950
Spike_AFFX-r2-P1-cre_avg-signal4054.997803
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.661552
Spike_AFFX-r2-Bs-thr_3_signal66.528130
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-signal27.266006
Spike_AFFX-r2-Bs-dap_3_signal202.150513
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.795357
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal205.964813
#M379
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal33.620716
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.156185
Spike_AFFX-r2-Bs-thr_M_signal43.555378
Signal(P)218.626251
Spike_AFFX-r2-Bs-phe_3-5-ratio1.452275
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7401,Count:9
Spike_AFFX-r2-P1-cre_5_signal3615.943848
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7320
Signal(M)12.863433
BackgroundAvg:56.07,Std:0.70,Min:54.4,Max:58.0
Spike_AFFX-r2-Ec-bioC_avg-signal222.049149
Spike_AFFX-r2-Bs-dap_avg-signal129.441833
Spike_AFFX-r2-Bs-dap_3-5-ratio3.956339
Spike_AFFX-r2-Ec-bioB_5_signal63.169781
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.494252
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-9_Col_52h_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-9_Col_52h_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-9_Col_52h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-4 (Columbia)
Stock Code: N933
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole 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:0.569749
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-ratio1.184045
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.087198
Spike_AFFX-r2-Bs-dap_5_signal71.287560
NoiseAvg:2.55,Std:0.10,Min:2.3,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal19.369761
#P14975
Spike_AFFX-r2-Bs-phe_M_signal23.960936
Corner-Avg:15518,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal86.648254
Spike_AFFX-r2-Ec-bioB_3_signal62.226192
Spike_AFFX-r2-Bs-lys_M_signal15.953608
Spike_AFFX-r2-P1-cre_3_signal4126.109863
Spike_AFFX-r2-Bs-lys_3-5-ratio2.404583
Spike_AFFX-r2-Bs-dap_M_signal124.899895
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.979244
Spike_AFFX-r2-Ec-bioB_avg-signal68.703270
Spike_AFFX-r2-Bs-thr_avg-signal47.416004
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal683.153931
Spike_AFFX-r2-Bs-phe_5_signal30.738937
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1172.558960
RawQ2.343663
Spike_AFFX-r2-Bs-lys_5_signal13.899381
Signal(A)3.721580
%A32.775097
Signal(All)140.582306
Corner+Avg:232,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal211.320557
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal34.773888
Spike_AFFX-r2-Ec-bioD_avg-signal927.856445
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.651031
Spike_AFFX-r2-Bs-lys_avg-signal21.091734
Spike_AFFX-r2-P1-cre_avg-signal3805.433838
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.573871
Spike_AFFX-r2-Bs-thr_3_signal77.077011
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-signal29.824587
Spike_AFFX-r2-Bs-dap_3_signal203.012680
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.716391
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal217.643646
#M359
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal33.422215
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.970948
Spike_AFFX-r2-Bs-thr_M_signal45.801235
Signal(P)211.962524
Spike_AFFX-r2-Bs-phe_3-5-ratio1.131265
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11040,Count:9
Spike_AFFX-r2-P1-cre_5_signal3484.757813
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7476
Signal(M)13.150778
BackgroundAvg:55.36,Std:0.69,Min:53.4,Max:57.4
Spike_AFFX-r2-Ec-bioC_avg-signal214.482101
Spike_AFFX-r2-Bs-dap_avg-signal133.066711
Spike_AFFX-r2-Bs-dap_3-5-ratio2.847800
Spike_AFFX-r2-Ec-bioB_5_signal57.235367
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.569749
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-10_bru1_contr_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-10_bru1_contr_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-10_bru1_contr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: bru1-2
Stock Code:
Genetic Background: Col-1
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At3g18730
Tissue: whole plant
Additional Organism Information:
Sample Descriptionwhole 3d old seedling
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:0.35289
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-ratio1.417115
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.237510
Spike_AFFX-r2-Bs-dap_5_signal62.872158
NoiseAvg:2.85,Std:0.05,Min:2.7,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.402620
#P15681
Spike_AFFX-r2-Bs-phe_M_signal22.797935
Corner-Avg:15639,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal63.462669
Spike_AFFX-r2-Ec-bioB_3_signal53.513401
Spike_AFFX-r2-Bs-lys_M_signal10.206940
Spike_AFFX-r2-P1-cre_3_signal3578.553711
Spike_AFFX-r2-Bs-lys_3-5-ratio1.739499
Spike_AFFX-r2-Bs-dap_M_signal138.178116
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.185069
Spike_AFFX-r2-Ec-bioB_avg-signal53.406292
Spike_AFFX-r2-Bs-thr_avg-signal34.112865
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal521.718140
Spike_AFFX-r2-Bs-phe_5_signal22.763165
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal856.045227
RawQ2.410931
Spike_AFFX-r2-Bs-lys_5_signal15.726224
Signal(A)2.886130
%A29.820253
Signal(All)138.583954
Corner+Avg:231,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal165.888000
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal46.401463
Spike_AFFX-r2-Ec-bioD_avg-signal688.881714
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.746162
Spike_AFFX-r2-Bs-lys_avg-signal17.762972
Spike_AFFX-r2-P1-cre_avg-signal3051.896484
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.433582
Spike_AFFX-r2-Bs-thr_3_signal44.581135
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-signal30.654190
Spike_AFFX-r2-Bs-dap_3_signal190.912827
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.640819
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal155.246201
#M327
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.355749
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.068548
Spike_AFFX-r2-Bs-thr_M_signal37.354836
Signal(P)200.083984
Spike_AFFX-r2-Bs-phe_3-5-ratio2.038445
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13146,Count:9
Spike_AFFX-r2-P1-cre_5_signal2525.239502
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6802
Signal(M)12.084444
BackgroundAvg:58.87,Std:0.50,Min:57.4,Max:60.1
Spike_AFFX-r2-Ec-bioC_avg-signal160.567108
Spike_AFFX-r2-Bs-dap_avg-signal130.654373
Spike_AFFX-r2-Bs-dap_3-5-ratio3.036524
Spike_AFFX-r2-Ec-bioB_5_signal43.242798
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.352890
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-11_bru1_contr_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-11_bru1_contr_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-11_bru1_contr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: bru1-2
Stock Code:
Genetic Background: Col-1
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At3g18730
Tissue: whole plant
Additional Organism Information:
Sample Descriptionwhole 3d old seedling
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:0.564241
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-ratio1.219620
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.126249
Spike_AFFX-r2-Bs-dap_5_signal12.023992
NoiseAvg:2.76,Std:0.14,Min:2.4,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.175178
#P14922
Spike_AFFX-r2-Bs-phe_M_signal25.294384
Corner-Avg:16021,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal87.830132
Spike_AFFX-r2-Ec-bioB_3_signal70.647461
Spike_AFFX-r2-Bs-lys_M_signal12.982300
Spike_AFFX-r2-P1-cre_3_signal3932.626709
Spike_AFFX-r2-Bs-lys_3-5-ratio1.597678
Spike_AFFX-r2-Bs-dap_M_signal82.066757
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.141285
Spike_AFFX-r2-Ec-bioB_avg-signal73.735229
Spike_AFFX-r2-Bs-thr_avg-signal30.529961
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal586.084351
Spike_AFFX-r2-Bs-phe_5_signal17.138901
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1146.847534
RawQ2.521680
Spike_AFFX-r2-Bs-lys_5_signal18.025593
Signal(A)4.282160
%A32.665497
Signal(All)145.122940
Corner+Avg:236,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal238.990005
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal41.142212
Spike_AFFX-r2-Ec-bioD_avg-signal866.465942
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.418678
Spike_AFFX-r2-Bs-lys_avg-signal19.935663
Spike_AFFX-r2-P1-cre_avg-signal3578.547363
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.915826
Spike_AFFX-r2-Bs-thr_3_signal42.138309
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-signal27.858500
Spike_AFFX-r2-Bs-dap_3_signal174.357651
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.956796
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal231.903214
#M437
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.799093
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.030559
Spike_AFFX-r2-Bs-thr_M_signal39.276390
Signal(P)219.223557
Spike_AFFX-r2-Bs-phe_3-5-ratio2.400516
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13576,Count:9
Spike_AFFX-r2-P1-cre_5_signal3224.467773
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7451
Signal(M)16.233173
BackgroundAvg:61.31,Std:0.82,Min:59.4,Max:63.3
Spike_AFFX-r2-Ec-bioC_avg-signal235.446609
Spike_AFFX-r2-Bs-dap_avg-signal89.482796
Spike_AFFX-r2-Bs-dap_3-5-ratio14.500813
Spike_AFFX-r2-Ec-bioB_5_signal62.728096
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.564241
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-12_bru1_contr_Rep3_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Baurle_562-12_bru1_contr_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-12_bru1_contr_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: bru1-2
Stock Code:
Genetic Background: Col-1
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At3g18730
Tissue: whole plant
Additional Organism Information:
Sample Descriptionwhole 3d old seedling
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:0.408938
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-ratio1.298663
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.444852
Spike_AFFX-r2-Bs-dap_5_signal90.699333
NoiseAvg:3.00,Std:0.07,Min:2.8,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal28.224590
#P15356
Spike_AFFX-r2-Bs-phe_M_signal24.062441
Corner-Avg:16857,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal78.869217
Spike_AFFX-r2-Ec-bioB_3_signal63.845615
Spike_AFFX-r2-Bs-lys_M_signal17.231203
Spike_AFFX-r2-P1-cre_3_signal4105.694824
Spike_AFFX-r2-Bs-lys_3-5-ratio1.697531
Spike_AFFX-r2-Bs-dap_M_signal176.407242
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.224608
Spike_AFFX-r2-Ec-bioB_avg-signal62.301056
Spike_AFFX-r2-Bs-thr_avg-signal48.191345
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal654.452820
Spike_AFFX-r2-Bs-phe_5_signal32.416954
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1041.676025
RawQ2.606691
Spike_AFFX-r2-Bs-lys_5_signal18.445990
Signal(A)3.372677
%A30.854889
Signal(All)141.339462
Corner+Avg:246,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal240.656540
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal41.629864
Spike_AFFX-r2-Ec-bioD_avg-signal848.064453
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.321350
Spike_AFFX-r2-Bs-lys_avg-signal22.329943
Spike_AFFX-r2-P1-cre_avg-signal3633.585938
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.823761
Spike_AFFX-r2-Bs-thr_3_signal62.788651
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-signal32.703087
Spike_AFFX-r2-Bs-dap_3_signal218.705765
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.591675
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal186.214218
#M416
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal31.312635
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.292364
Spike_AFFX-r2-Bs-thr_M_signal53.560787
Signal(P)208.058105
Spike_AFFX-r2-Bs-phe_3-5-ratio1.284200
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14660,Count:9
Spike_AFFX-r2-P1-cre_5_signal3161.477295
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7038
Signal(M)12.682589
BackgroundAvg:63.79,Std:0.60,Min:62.1,Max:65.3
Spike_AFFX-r2-Ec-bioC_avg-signal213.435379
Spike_AFFX-r2-Bs-dap_avg-signal161.937454
Spike_AFFX-r2-Bs-dap_3-5-ratio2.411327
Spike_AFFX-r2-Ec-bioB_5_signal44.188347
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.408938
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-13_bru1_4h_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-13_bru1_4h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-13_bru1_4h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: bru1-2
Stock Code:
Genetic Background: Col-1
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At3g18730
Tissue: whole 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:0.513833
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-ratio1.058154
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.051764
Spike_AFFX-r2-Bs-dap_5_signal110.443222
NoiseAvg:2.86,Std:0.15,Min:2.6,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal28.620161
#P15081
Spike_AFFX-r2-Bs-phe_M_signal33.653275
Corner-Avg:18076,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal124.852173
Spike_AFFX-r2-Ec-bioB_3_signal82.552177
Spike_AFFX-r2-Bs-lys_M_signal21.422169
Spike_AFFX-r2-P1-cre_3_signal4007.900391
Spike_AFFX-r2-Bs-lys_3-5-ratio1.518775
Spike_AFFX-r2-Bs-dap_M_signal226.958023
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.700980
Spike_AFFX-r2-Ec-bioB_avg-signal95.297874
Spike_AFFX-r2-Bs-thr_avg-signal68.360336
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal782.104553
Spike_AFFX-r2-Bs-phe_5_signal34.623875
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1349.142700
RawQ2.655088
Spike_AFFX-r2-Bs-lys_5_signal29.877081
Signal(A)3.527177
%A32.306007
Signal(All)139.110321
Corner+Avg:276,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal300.899750
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal48.740082
Spike_AFFX-r2-Ec-bioD_avg-signal1065.623657
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.115738
Spike_AFFX-r2-Bs-lys_avg-signal32.225269
Spike_AFFX-r2-P1-cre_avg-signal3897.767090
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.578255
Spike_AFFX-r2-Bs-thr_3_signal105.922653
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-signal39.005741
Spike_AFFX-r2-Bs-dap_3_signal293.718842
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.725016
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal269.625824
#M360
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal45.376560
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.115990
Spike_AFFX-r2-Bs-thr_M_signal70.538200
Signal(P)208.358902
Spike_AFFX-r2-Bs-phe_3-5-ratio1.407701
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15591,Count:9
Spike_AFFX-r2-P1-cre_5_signal3787.634033
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7369
Signal(M)13.483648
BackgroundAvg:61.69,Std:0.74,Min:60.2,Max:63.7
Spike_AFFX-r2-Ec-bioC_avg-signal285.262787
Spike_AFFX-r2-Bs-dap_avg-signal210.373367
Spike_AFFX-r2-Bs-dap_3-5-ratio2.659456
Spike_AFFX-r2-Ec-bioB_5_signal78.489250
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.513833
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-14_bru1_4h_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-14_bru1_4h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-14_bru1_4h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: bru1-2
Stock Code:
Genetic Background: Col-1
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At3g18730
Tissue: whole 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:0.353625
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-ratio1.271903
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.179783
Spike_AFFX-r2-Bs-dap_5_signal89.752068
NoiseAvg:3.42,Std:0.12,Min:3.2,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal24.449371
#P15454
Spike_AFFX-r2-Bs-phe_M_signal31.634453
Corner-Avg:19423,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal86.215080
Spike_AFFX-r2-Ec-bioB_3_signal66.960648
Spike_AFFX-r2-Bs-lys_M_signal13.616797
Spike_AFFX-r2-P1-cre_3_signal3592.348145
Spike_AFFX-r2-Bs-lys_3-5-ratio1.746899
Spike_AFFX-r2-Bs-dap_M_signal177.881546
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.664749
Spike_AFFX-r2-Ec-bioB_avg-signal69.977486
Spike_AFFX-r2-Bs-thr_avg-signal52.670101
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal698.261597
Spike_AFFX-r2-Bs-phe_5_signal34.259930
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1119.359497
RawQ2.761159
Spike_AFFX-r2-Bs-lys_5_signal19.689449
Signal(A)3.171936
%A30.578693
Signal(All)136.643478
Corner+Avg:302,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal245.661102
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal44.470444
Spike_AFFX-r2-Ec-bioD_avg-signal908.810547
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.750984
Spike_AFFX-r2-Bs-lys_avg-signal22.567240
Spike_AFFX-r2-P1-cre_avg-signal3208.368164
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.670320
Spike_AFFX-r2-Bs-thr_3_signal89.600815
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-signal36.788273
Spike_AFFX-r2-Bs-dap_3_signal252.381317
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.603066
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal219.691849
#M381
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal34.395470
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.118208
Spike_AFFX-r2-Bs-thr_M_signal43.960117
Signal(P)199.966446
Spike_AFFX-r2-Bs-phe_3-5-ratio1.298031
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15591,Count:9
Spike_AFFX-r2-P1-cre_5_signal2824.388428
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6975
Signal(M)11.632768
BackgroundAvg:67.08,Std:0.38,Min:66.0,Max:68.2
Spike_AFFX-r2-Ec-bioC_avg-signal232.676483
Spike_AFFX-r2-Bs-dap_avg-signal173.338318
Spike_AFFX-r2-Bs-dap_3-5-ratio2.811983
Spike_AFFX-r2-Ec-bioB_5_signal56.756725
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.353625
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-15_bru1_4h_Rep3_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Baurle_562-15_bru1_4h_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-15_bru1_4h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: bru1-2
Stock Code:
Genetic Background: Col-1
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At3g18730
Tissue: whole 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:0.517073
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-ratio1.270821
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.272849
Spike_AFFX-r2-Bs-dap_5_signal90.016350
NoiseAvg:3.01,Std:0.11,Min:2.7,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal31.895624
#P14875
Spike_AFFX-r2-Bs-phe_M_signal32.774193
Corner-Avg:16404,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal93.676857
Spike_AFFX-r2-Ec-bioB_3_signal62.413029
Spike_AFFX-r2-Bs-lys_M_signal17.102438
Spike_AFFX-r2-P1-cre_3_signal4134.201660
Spike_AFFX-r2-Bs-lys_3-5-ratio1.523332
Spike_AFFX-r2-Bs-dap_M_signal260.338867
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.526765
Spike_AFFX-r2-Ec-bioB_avg-signal68.374672
Spike_AFFX-r2-Bs-thr_avg-signal71.905144
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal675.867310
Spike_AFFX-r2-Bs-phe_5_signal40.658562
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1151.851807
RawQ2.581995
Spike_AFFX-r2-Bs-lys_5_signal25.484953
Signal(A)3.905170
%A33.095135
Signal(All)140.626801
Corner+Avg:239,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal252.202713
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal44.866306
Spike_AFFX-r2-Ec-bioD_avg-signal913.859558
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.212624
Spike_AFFX-r2-Bs-lys_avg-signal27.136477
Spike_AFFX-r2-P1-cre_avg-signal3693.687256
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.692240
Spike_AFFX-r2-Bs-thr_3_signal112.488380
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-signal39.433022
Spike_AFFX-r2-Bs-dap_3_signal342.472931
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.704257
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal249.926376
#M386
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal38.822037
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.009108
Spike_AFFX-r2-Bs-thr_M_signal71.331413
Signal(P)213.298050
Spike_AFFX-r2-Bs-phe_3-5-ratio1.103490
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14105,Count:9
Spike_AFFX-r2-P1-cre_5_signal3253.172852
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7549
Signal(M)14.012196
BackgroundAvg:61.58,Std:0.62,Min:59.3,Max:63.0
Spike_AFFX-r2-Ec-bioC_avg-signal251.064545
Spike_AFFX-r2-Bs-dap_avg-signal230.942703
Spike_AFFX-r2-Bs-dap_3-5-ratio3.804564
Spike_AFFX-r2-Ec-bioB_5_signal49.034122
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.517073
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-16_bru1_52h_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-16_bru1_52h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-16_bru1_52h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: bru1-2
Stock Code:
Genetic Background: Col-1
Age: 5 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: EMS induced mutation mutation in At3g18730
Tissue: whole 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:0.43246
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-ratio1.221631
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.244035
Spike_AFFX-r2-Bs-dap_5_signal95.481560
NoiseAvg:3.09,Std:0.10,Min:2.8,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal25.179838
#P14963
Spike_AFFX-r2-Bs-phe_M_signal26.026550
Corner-Avg:20451,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal83.004799
Spike_AFFX-r2-Ec-bioB_3_signal80.545319
Spike_AFFX-r2-Bs-lys_M_signal11.143833
Spike_AFFX-r2-P1-cre_3_signal4066.549805
Spike_AFFX-r2-Bs-lys_3-5-ratio2.769334
Spike_AFFX-r2-Bs-dap_M_signal186.864868
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.163672
Spike_AFFX-r2-Ec-bioB_avg-signal76.098434
Spike_AFFX-r2-Bs-thr_avg-signal50.367161
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal723.399841
Spike_AFFX-r2-Bs-phe_5_signal32.566151
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1222.218994
RawQ2.730704
Spike_AFFX-r2-Bs-lys_5_signal16.522919
Signal(A)3.623156
%A32.823322
Signal(All)139.947037
Corner+Avg:324,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal238.876251
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.692528
Spike_AFFX-r2-Ec-bioD_avg-signal972.809448
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.598419
Spike_AFFX-r2-Bs-lys_avg-signal24.474745
Spike_AFFX-r2-P1-cre_avg-signal3697.668213
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.578255
Spike_AFFX-r2-Bs-thr_3_signal79.660751
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-signal26.761744
Spike_AFFX-r2-Bs-dap_3_signal261.333099
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.689548
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal214.143112
#M360
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal45.757481
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.115498
Spike_AFFX-r2-Bs-thr_M_signal46.260902
Signal(P)211.160980
Spike_AFFX-r2-Bs-phe_3-5-ratio0.666107
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15756,Count:9
Spike_AFFX-r2-P1-cre_5_signal3328.786621
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7487
Signal(M)15.176289
BackgroundAvg:64.39,Std:0.70,Min:62.5,Max:66.2
Spike_AFFX-r2-Ec-bioC_avg-signal226.509674
Spike_AFFX-r2-Bs-dap_avg-signal181.226501
Spike_AFFX-r2-Bs-dap_3-5-ratio2.737001
Spike_AFFX-r2-Ec-bioB_5_signal64.745193
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.432460
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-17_bru1_52h_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-17_bru1_52h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-17_bru1_52h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: bru1-2
Stock Code:
Genetic Background: Col-1
Age: 5 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: EMS induced mutation mutation in At3g18730
Tissue: whole 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:0.545151
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-ratio1.218054
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.055795
Spike_AFFX-r2-Bs-dap_5_signal110.561279
NoiseAvg:3.02,Std:0.11,Min:2.9,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_signal23.573956
#P14677
Spike_AFFX-r2-Bs-phe_M_signal25.699196
Corner-Avg:16317,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal88.392975
Spike_AFFX-r2-Ec-bioB_3_signal71.547729
Spike_AFFX-r2-Bs-lys_M_signal16.943775
Spike_AFFX-r2-P1-cre_3_signal4018.414307
Spike_AFFX-r2-Bs-lys_3-5-ratio1.746732
Spike_AFFX-r2-Bs-dap_M_signal196.664276
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.186217
Spike_AFFX-r2-Ec-bioB_avg-signal75.902466
Spike_AFFX-r2-Bs-thr_avg-signal59.157425
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal733.760498
Spike_AFFX-r2-Bs-phe_5_signal27.288681
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1253.936157
RawQ2.744824
Spike_AFFX-r2-Bs-lys_5_signal21.075377
Signal(A)4.338716
%A33.805347
Signal(All)143.140060
Corner+Avg:241,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal264.831268
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal44.149956
Spike_AFFX-r2-Ec-bioD_avg-signal993.848328
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.344589
Spike_AFFX-r2-Bs-lys_avg-signal24.944059
Spike_AFFX-r2-P1-cre_avg-signal3658.729004
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.850066
Spike_AFFX-r2-Bs-thr_3_signal98.685692
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-signal32.379276
Spike_AFFX-r2-Bs-dap_3_signal241.009659
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.708917
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal258.363983
#M422
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal36.813026
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.025032
Spike_AFFX-r2-Bs-thr_M_signal55.212620
Signal(P)219.736572
Spike_AFFX-r2-Bs-phe_3-5-ratio1.617885
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12385,Count:9
Spike_AFFX-r2-P1-cre_5_signal3299.043945
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7711
Signal(M)15.391571
BackgroundAvg:65.17,Std:0.80,Min:62.9,Max:67.3
Spike_AFFX-r2-Ec-bioC_avg-signal261.597626
Spike_AFFX-r2-Bs-dap_avg-signal182.745071
Spike_AFFX-r2-Bs-dap_3-5-ratio2.179874
Spike_AFFX-r2-Ec-bioB_5_signal67.766701
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.545151
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-18_bru1_52h_Rep3_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Baurle_562-18_bru1_52h_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-18_bru1_52h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: bru1-2
Stock Code:
Genetic Background: Col-1
Age: 5 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: EMS induced mutation mutation in At3g18730
Tissue: whole 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:0.369592
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-ratio1.329637
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.261215
Spike_AFFX-r2-Bs-dap_5_signal84.535843
NoiseAvg:3.59,Std:0.08,Min:3.4,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal25.313925
#P15193
Spike_AFFX-r2-Bs-phe_M_signal18.453251
Corner-Avg:18813,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal72.930580
Spike_AFFX-r2-Ec-bioB_3_signal60.011444
Spike_AFFX-r2-Bs-lys_M_signal10.045976
Spike_AFFX-r2-P1-cre_3_signal3237.110107
Spike_AFFX-r2-Bs-lys_3-5-ratio1.729961
Spike_AFFX-r2-Bs-dap_M_signal169.885086
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.478483
Spike_AFFX-r2-Ec-bioB_avg-signal60.174755
Spike_AFFX-r2-Bs-thr_avg-signal45.095959
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal543.441162
Spike_AFFX-r2-Bs-phe_5_signal26.041168
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal960.476624
RawQ3.048565
Spike_AFFX-r2-Bs-lys_5_signal15.858356
Signal(A)3.461980
%A31.740465
Signal(All)137.468704
Corner+Avg:296,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal220.450500
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal36.268440
Spike_AFFX-r2-Ec-bioD_avg-signal751.958862
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.606750
Spike_AFFX-r2-Bs-lys_avg-signal17.779556
Spike_AFFX-r2-P1-cre_avg-signal2835.845703
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.652784
Spike_AFFX-r2-Bs-thr_3_signal62.740124
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-signal26.920954
Spike_AFFX-r2-Bs-dap_3_signal183.089569
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.767398
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal191.257431
#M377
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.434338
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.152638
Spike_AFFX-r2-Bs-thr_M_signal47.233829
Signal(P)204.427078
Spike_AFFX-r2-Bs-phe_3-5-ratio1.392735
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15842,Count:9
Spike_AFFX-r2-P1-cre_5_signal2434.581299
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7240
Signal(M)12.562481
BackgroundAvg:74.84,Std:0.93,Min:71.8,Max:77.2
Spike_AFFX-r2-Ec-bioC_avg-signal205.853973
Spike_AFFX-r2-Bs-dap_avg-signal145.836838
Spike_AFFX-r2-Bs-dap_3-5-ratio2.165822
Spike_AFFX-r2-Ec-bioB_5_signal47.582249
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.369592
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-19_ago1_contr_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-19_ago1_contr_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-19_ago1_contr_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: ago1-25
Stock Code:
Genetic Background: Col-1
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At1g48410
Tissue: whole plant
Additional Organism Information:
Sample Descriptionwhole 3d old seedling
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:0.290305
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-ratio1.322627
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.276268
Spike_AFFX-r2-Bs-dap_5_signal86.996666
NoiseAvg:4.00,Std:0.13,Min:3.7,Max:4.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal22.779400
#P15644
Spike_AFFX-r2-Bs-phe_M_signal28.894560
Corner-Avg:22206,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal71.642723
Spike_AFFX-r2-Ec-bioB_3_signal54.985455
Spike_AFFX-r2-Bs-lys_M_signal16.937086
Spike_AFFX-r2-P1-cre_3_signal3210.805908
Spike_AFFX-r2-Bs-lys_3-5-ratio1.715371
Spike_AFFX-r2-Bs-dap_M_signal154.075562
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.161674
Spike_AFFX-r2-Ec-bioB_avg-signal56.570389
Spike_AFFX-r2-Bs-thr_avg-signal38.564495
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal554.279358
Spike_AFFX-r2-Bs-phe_5_signal23.112371
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal970.238342
RawQ3.032532
Spike_AFFX-r2-Bs-lys_5_signal16.061823
Signal(A)3.252145
%A29.982464
Signal(All)138.392700
Corner+Avg:361,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal193.524139
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal41.046547
Spike_AFFX-r2-Ec-bioD_avg-signal762.258850
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.583954
Spike_AFFX-r2-Bs-lys_avg-signal20.183632
Spike_AFFX-r2-P1-cre_avg-signal2819.201660
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.433582
Spike_AFFX-r2-Bs-thr_3_signal49.241631
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal31.017828
Spike_AFFX-r2-Bs-dap_3_signal208.575211
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.750450
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal178.734711
#M327
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.551985
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.082745
Spike_AFFX-r2-Bs-thr_M_signal43.672455
Signal(P)200.092514
Spike_AFFX-r2-Bs-phe_3-5-ratio1.775956
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:17875,Count:9
Spike_AFFX-r2-P1-cre_5_signal2427.597656
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6839
Signal(M)12.993719
BackgroundAvg:75.52,Std:0.98,Min:72.7,Max:77.8
Spike_AFFX-r2-Ec-bioC_avg-signal186.129425
Spike_AFFX-r2-Bs-dap_avg-signal149.882477
Spike_AFFX-r2-Bs-dap_3-5-ratio2.397508
Spike_AFFX-r2-Ec-bioB_5_signal43.082996
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.290305
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-20_ago1_contr_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Baurle_562-20_ago1_contr_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-20_ago1_contr_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: ago1-25
Stock Code:
Genetic Background: Col-1
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At1g48410
Tissue: whole plant
Additional Organism Information:
Sample Descriptionwhole 3d old seedling
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:0.298834
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-ratio1.229355
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.184422
Spike_AFFX-r2-Bs-dap_5_signal74.459312
NoiseAvg:4.26,Std:0.20,Min:3.7,Max:4.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal14.714183
#P15671
Spike_AFFX-r2-Bs-phe_M_signal26.984699
Corner-Avg:20174,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal47.337521
Spike_AFFX-r2-Ec-bioB_3_signal46.372410
Spike_AFFX-r2-Bs-lys_M_signal12.067294
Spike_AFFX-r2-P1-cre_3_signal2671.296143
Spike_AFFX-r2-Bs-lys_3-5-ratio1.560367
Spike_AFFX-r2-Bs-dap_M_signal139.190109
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.706135
Spike_AFFX-r2-Ec-bioB_avg-signal44.287289
Spike_AFFX-r2-Bs-thr_avg-signal36.841228
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal454.239410
Spike_AFFX-r2-Bs-phe_5_signal21.538534
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal755.290955
RawQ3.265049
Spike_AFFX-r2-Bs-lys_5_signal15.162961
Signal(A)3.375442
%A29.723804
Signal(All)136.580353
Corner+Avg:320,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal162.743057
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal35.536949
Spike_AFFX-r2-Ec-bioD_avg-signal604.765198
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.702324
Spike_AFFX-r2-Bs-lys_avg-signal16.963345
Spike_AFFX-r2-P1-cre_avg-signal2422.110840
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.573871
Spike_AFFX-r2-Bs-thr_3_signal54.532749
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-signal28.020060
Spike_AFFX-r2-Bs-dap_3_signal171.586349
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.662760
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal144.744507
#M359
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.659781
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.124347
Spike_AFFX-r2-Bs-thr_M_signal41.276752
Signal(P)197.061646
Spike_AFFX-r2-Bs-phe_3-5-ratio1.649924
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15239,Count:9
Spike_AFFX-r2-P1-cre_5_signal2172.925537
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6780
Signal(M)12.143124
BackgroundAvg:84.03,Std:0.95,Min:81.8,Max:86.2
Spike_AFFX-r2-Ec-bioC_avg-signal153.743774
Spike_AFFX-r2-Bs-dap_avg-signal128.411926
Spike_AFFX-r2-Bs-dap_3-5-ratio2.304431
Spike_AFFX-r2-Ec-bioB_5_signal39.151936
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.298834
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-21_ago1_contr_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-21_ago1_contr_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-21_ago1_contr_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: ago1-25
Stock Code:
Genetic Background: Col-1
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At1g48410
Tissue: whole plant
Additional Organism Information:
Sample Descriptionwhole 3d old seedling
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:0.369946
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-ratio1.110616
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.428187
Spike_AFFX-r2-Bs-dap_5_signal54.727882
NoiseAvg:3.49,Std:0.15,Min:2.9,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.087393
#P15849
Spike_AFFX-r2-Bs-phe_M_signal14.163975
Corner-Avg:18688,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal56.990028
Spike_AFFX-r2-Ec-bioB_3_signal53.337261
Spike_AFFX-r2-Bs-lys_M_signal10.771801
Spike_AFFX-r2-P1-cre_3_signal2417.063721
Spike_AFFX-r2-Bs-lys_3-5-ratio1.821521
Spike_AFFX-r2-Bs-dap_M_signal117.975121
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.141115
Spike_AFFX-r2-Ec-bioB_avg-signal49.224476
Spike_AFFX-r2-Bs-thr_avg-signal36.412785
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal385.127625
Spike_AFFX-r2-Bs-phe_5_signal23.793463
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal700.253235
RawQ2.921230
Spike_AFFX-r2-Bs-lys_5_signal10.161386
Signal(A)3.387621
%A29.004822
Signal(All)135.548065
Corner+Avg:287,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal157.373978
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.111252
Spike_AFFX-r2-Ec-bioD_avg-signal542.690430
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.482681
Spike_AFFX-r2-Bs-lys_avg-signal13.147454
Spike_AFFX-r2-P1-cre_avg-signal2296.695801
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.512495
Spike_AFFX-r2-Bs-thr_3_signal50.532345
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-signal22.022896
Spike_AFFX-r2-Bs-dap_3_signal157.361282
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.818237
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal133.845245
#M345
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.509176
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.175791
Spike_AFFX-r2-Bs-thr_M_signal42.618618
Signal(P)193.409027
Spike_AFFX-r2-Bs-phe_3-5-ratio1.181470
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14841,Count:9
Spike_AFFX-r2-P1-cre_5_signal2176.327881
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6616
Signal(M)11.881763
BackgroundAvg:68.45,Std:1.24,Min:65.4,Max:71.6
Spike_AFFX-r2-Ec-bioC_avg-signal145.609619
Spike_AFFX-r2-Bs-dap_avg-signal110.021423
Spike_AFFX-r2-Bs-dap_3-5-ratio2.875340
Spike_AFFX-r2-Ec-bioB_5_signal37.346142
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.369946
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-22_ago1_4h_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-22_ago1_4h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-22_ago1_4h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: ago1-25
Stock Code:
Genetic Background: Col-1
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At1g48410
Tissue: whole 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:0.632396
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-ratio1.149715
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.289033
Spike_AFFX-r2-Bs-dap_5_signal92.874474
NoiseAvg:2.64,Std:0.05,Min:2.4,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_signal19.498631
#P15259
Spike_AFFX-r2-Bs-phe_M_signal30.363117
Corner-Avg:15446,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal107.643082
Spike_AFFX-r2-Ec-bioB_3_signal87.718513
Spike_AFFX-r2-Bs-lys_M_signal17.109489
Spike_AFFX-r2-P1-cre_3_signal4454.186035
Spike_AFFX-r2-Bs-lys_3-5-ratio1.830123
Spike_AFFX-r2-Bs-dap_M_signal185.277252
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.907558
Spike_AFFX-r2-Ec-bioB_avg-signal87.803810
Spike_AFFX-r2-Bs-thr_avg-signal46.376926
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal624.143738
Spike_AFFX-r2-Bs-phe_5_signal24.839064
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1241.708374
RawQ2.491915
Spike_AFFX-r2-Bs-lys_5_signal16.881456
Signal(A)4.226314
%A31.494959
Signal(All)141.679810
Corner+Avg:228,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal278.380035
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal29.226973
Spike_AFFX-r2-Ec-bioD_avg-signal932.926025
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.896095
Spike_AFFX-r2-Bs-lys_avg-signal21.628695
Spike_AFFX-r2-P1-cre_avg-signal4164.176270
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.608943
Spike_AFFX-r2-Bs-thr_3_signal76.192024
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-signal28.143051
Spike_AFFX-r2-Bs-dap_3_signal259.887268
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.989459
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal263.145508
#M367
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal30.895144
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.057894
Spike_AFFX-r2-Bs-thr_M_signal43.440136
Signal(P)209.432007
Spike_AFFX-r2-Bs-phe_3-5-ratio1.176654
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12883,Count:9
Spike_AFFX-r2-P1-cre_5_signal3874.166748
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7184
Signal(M)15.344602
BackgroundAvg:59.40,Std:0.42,Min:57.7,Max:60.3
Spike_AFFX-r2-Ec-bioC_avg-signal270.762756
Spike_AFFX-r2-Bs-dap_avg-signal179.346329
Spike_AFFX-r2-Bs-dap_3-5-ratio2.798264
Spike_AFFX-r2-Ec-bioB_5_signal68.049835
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.632396
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-23_ago1_4h_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Baurle_562-23_ago1_4h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-23_ago1_4h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: ago1-25
Stock Code:
Genetic Background: Col-1
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At1g48410
Tissue: whole 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:0.562561
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.998973
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.831905
Spike_AFFX-r2-Bs-dap_5_signal76.448509
NoiseAvg:2.99,Std:0.25,Min:2.6,Max:4.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal28.957281
#P15219
Spike_AFFX-r2-Bs-phe_M_signal28.504189
Corner-Avg:17065,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal89.431465
Spike_AFFX-r2-Ec-bioB_3_signal59.053059
Spike_AFFX-r2-Bs-lys_M_signal15.047108
Spike_AFFX-r2-P1-cre_3_signal3837.199707
Spike_AFFX-r2-Bs-lys_3-5-ratio2.078603
Spike_AFFX-r2-Bs-dap_M_signal181.198944
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.673585
Spike_AFFX-r2-Ec-bioB_avg-signal73.156624
Spike_AFFX-r2-Bs-thr_avg-signal51.715378
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal770.968811
Spike_AFFX-r2-Bs-phe_5_signal26.278326
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1304.497681
RawQ2.641428
Spike_AFFX-r2-Bs-lys_5_signal20.826363
Signal(A)3.980116
%A31.556335
Signal(All)139.937912
Corner+Avg:263,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal286.083954
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal39.051655
Spike_AFFX-r2-Ec-bioD_avg-signal1037.733276
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.720734
Spike_AFFX-r2-Bs-lys_avg-signal26.387739
Spike_AFFX-r2-P1-cre_avg-signal3839.171875
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.722929
Spike_AFFX-r2-Bs-thr_3_signal77.419754
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal31.278059
Spike_AFFX-r2-Bs-dap_3_signal233.786285
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.692024
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal259.212280
#M393
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal43.289745
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.103667
Spike_AFFX-r2-Bs-thr_M_signal48.769104
Signal(P)207.476120
Spike_AFFX-r2-Bs-phe_3-5-ratio1.486079
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12704,Count:9
Spike_AFFX-r2-P1-cre_5_signal3841.143799
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7198
Signal(M)14.646369
BackgroundAvg:63.63,Std:0.75,Min:61.6,Max:65.5
Spike_AFFX-r2-Ec-bioC_avg-signal272.648132
Spike_AFFX-r2-Bs-dap_avg-signal163.811249
Spike_AFFX-r2-Bs-dap_3-5-ratio3.058088
Spike_AFFX-r2-Ec-bioB_5_signal70.985359
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.562561
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-24_ago1_4h_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-24_ago1_4h_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-24_ago1_4h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: ago1-25
Stock Code:
Genetic Background: Col-1
Age: 3 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At1g48410
Tissue: whole 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:0.484457
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-ratio1.206637
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.085174
Spike_AFFX-r2-Bs-dap_5_signal110.802444
NoiseAvg:3.00,Std:0.07,Min:2.8,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_signal28.989704
#P15225
Spike_AFFX-r2-Bs-phe_M_signal38.009819
Corner-Avg:17346,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal92.852463
Spike_AFFX-r2-Ec-bioB_3_signal58.921921
Spike_AFFX-r2-Bs-lys_M_signal17.796942
Spike_AFFX-r2-P1-cre_3_signal3920.243652
Spike_AFFX-r2-Bs-lys_3-5-ratio1.216325
Spike_AFFX-r2-Bs-dap_M_signal298.906982
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.707134
Spike_AFFX-r2-Ec-bioB_avg-signal68.690529
Spike_AFFX-r2-Bs-thr_avg-signal76.442276
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal666.899597
Spike_AFFX-r2-Bs-phe_5_signal53.193260
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1087.226929
RawQ2.654436
Spike_AFFX-r2-Bs-lys_5_signal33.813980
Signal(A)3.672434
%A31.727312
Signal(All)140.785736
Corner+Avg:263,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal252.884399
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal54.266705
Spike_AFFX-r2-Ec-bioD_avg-signal877.063232
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.747040
Spike_AFFX-r2-Bs-lys_avg-signal30.913239
Spike_AFFX-r2-P1-cre_avg-signal3584.572754
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.525647
Spike_AFFX-r2-Bs-thr_3_signal136.458435
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-signal48.489929
Spike_AFFX-r2-Bs-dap_3_signal318.326538
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.630271
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal240.824387
#M348
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal41.128796
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.050078
Spike_AFFX-r2-Bs-thr_M_signal63.878696
Signal(P)208.861816
Spike_AFFX-r2-Bs-phe_3-5-ratio1.020180
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12869,Count:9
Spike_AFFX-r2-P1-cre_5_signal3248.901611
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7237
Signal(M)13.861945
BackgroundAvg:64.06,Std:0.83,Min:61.1,Max:66.4
Spike_AFFX-r2-Ec-bioC_avg-signal246.854401
Spike_AFFX-r2-Bs-dap_avg-signal242.678650
Spike_AFFX-r2-Bs-dap_3-5-ratio2.872920
Spike_AFFX-r2-Ec-bioB_5_signal54.297207
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.484457
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-25_ago1_52h_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-25_ago1_52h_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-25_ago1_52h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: ago1-25
Stock Code:
Genetic Background: Col-1
Age: 5 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: EMS induced mutation mutation in At1g48410
Tissue: whole 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:0.384569
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-ratio1.336886
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.232049
Spike_AFFX-r2-Bs-dap_5_signal79.425392
NoiseAvg:3.67,Std:0.09,Min:3.4,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal21.700687
#P15292
Spike_AFFX-r2-Bs-phe_M_signal24.887012
Corner-Avg:18799,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal67.329666
Spike_AFFX-r2-Ec-bioB_3_signal72.431992
Spike_AFFX-r2-Bs-lys_M_signal14.698689
Spike_AFFX-r2-P1-cre_3_signal3433.256836
Spike_AFFX-r2-Bs-lys_3-5-ratio2.071210
Spike_AFFX-r2-Bs-dap_M_signal176.049774
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.591134
Spike_AFFX-r2-Ec-bioB_avg-signal66.183846
Spike_AFFX-r2-Bs-thr_avg-signal40.311954
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal546.677795
Spike_AFFX-r2-Bs-phe_5_signal18.251143
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal951.371643
RawQ3.048939
Spike_AFFX-r2-Bs-lys_5_signal14.983014
Signal(A)3.853215
%A31.280140
Signal(All)139.659592
Corner+Avg:290,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal208.454712
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal32.538960
Spike_AFFX-r2-Ec-bioD_avg-signal749.024719
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.040771
Spike_AFFX-r2-Bs-lys_avg-signal20.238226
Spike_AFFX-r2-P1-cre_avg-signal3000.678223
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.679088
Spike_AFFX-r2-Bs-thr_3_signal56.229397
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-signal25.225706
Spike_AFFX-r2-Bs-dap_3_signal210.997833
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.740279
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal199.863556
#M383
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal31.032976
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.042985
Spike_AFFX-r2-Bs-thr_M_signal43.005791
Signal(P)206.160034
Spike_AFFX-r2-Bs-phe_3-5-ratio1.782845
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15695,Count:9
Spike_AFFX-r2-P1-cre_5_signal2568.099365
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7135
Signal(M)14.473703
BackgroundAvg:75.06,Std:0.85,Min:72.7,Max:77.3
Spike_AFFX-r2-Ec-bioC_avg-signal204.159134
Spike_AFFX-r2-Bs-dap_avg-signal155.490997
Spike_AFFX-r2-Bs-dap_3-5-ratio2.656554
Spike_AFFX-r2-Ec-bioB_5_signal58.789883
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.384569
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-26_ago1_52h_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Baurle_562-26_ago1_52h_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-26_ago1_52h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: ago1-25
Stock Code:
Genetic Background: Col-1
Age: 5 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: EMS induced mutation mutation in At1g48410
Tissue: whole 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:0.532385
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-ratio1.108384
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.683838
Spike_AFFX-r2-Bs-dap_5_signal85.609062
NoiseAvg:3.23,Std:0.09,Min:3.1,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal21.059608
#P14972
Spike_AFFX-r2-Bs-phe_M_signal26.813984
Corner-Avg:16502,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal89.680771
Spike_AFFX-r2-Ec-bioB_3_signal91.258751
Spike_AFFX-r2-Bs-lys_M_signal15.696560
Spike_AFFX-r2-P1-cre_3_signal3531.519531
Spike_AFFX-r2-Bs-lys_3-5-ratio2.580030
Spike_AFFX-r2-Bs-dap_M_signal172.091171
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.650416
Spike_AFFX-r2-Ec-bioB_avg-signal78.378792
Spike_AFFX-r2-Bs-thr_avg-signal45.355946
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal599.825073
Spike_AFFX-r2-Bs-phe_5_signal36.745483
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1121.961914
RawQ2.896369
Spike_AFFX-r2-Bs-lys_5_signal15.893523
Signal(A)4.525446
%A32.520824
Signal(All)143.011703
Corner+Avg:242,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal265.570038
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal39.381672
Spike_AFFX-r2-Ec-bioD_avg-signal860.893494
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.637878
Spike_AFFX-r2-Bs-lys_avg-signal24.198616
Spike_AFFX-r2-P1-cre_avg-signal3358.854004
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.841298
Spike_AFFX-r2-Bs-thr_3_signal55.816730
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-signal34.313713
Spike_AFFX-r2-Bs-dap_3_signal216.607651
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.870482
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal210.042740
#M420
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal41.005764
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.264362
Spike_AFFX-r2-Bs-thr_M_signal59.191505
Signal(P)215.175781
Spike_AFFX-r2-Bs-phe_3-5-ratio1.071742
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14793,Count:9
Spike_AFFX-r2-P1-cre_5_signal3186.188232
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7418
Signal(M)16.465019
BackgroundAvg:70.47,Std:0.97,Min:68.3,Max:73.0
Spike_AFFX-r2-Ec-bioC_avg-signal237.806396
Spike_AFFX-r2-Bs-dap_avg-signal158.102631
Spike_AFFX-r2-Bs-dap_3-5-ratio2.530195
Spike_AFFX-r2-Ec-bioB_5_signal54.196854
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.532385
NF1.000000
HZ4
Tau0.015000

Slide: Baurle_562-27_ago1_52h_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Baurle_562-27_ago1_52h_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Baurle_562-27_ago1_52h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: ago1-25
Stock Code:
Genetic Background: Col-1
Age: 5 days
Growth Conditions:
Stratification3d at 4C
SterilisationIncubate seeds 5 min in 50% sodium hypochlorite, followed by 3 washes with 100% EtOH. Allow seed to dry
ProtocolSeeds were plated on GM agar. After stratification plates were incubated at 23C in long days (16hr photoperiod).
Percentage Agrose0.9
Substrate Sterilising Procedurestandard autoclaving (steam/121C)
Plant Spacing60 per plate
Temperature23 °C average, 23 °C day, 23 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Phillips. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.02
Genetic Variation: EMS induced mutation mutation in At1g48410
Tissue: whole 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:0.380049
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-ratio1.355815
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.409633
Spike_AFFX-r2-Bs-dap_5_signal98.537003
NoiseAvg:4.01,Std:0.13,Min:3.7,Max:4.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal21.894482
#P15087
Spike_AFFX-r2-Bs-phe_M_signal26.125431
Corner-Avg:19246,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal61.369789
Spike_AFFX-r2-Ec-bioB_3_signal58.021976
Spike_AFFX-r2-Bs-lys_M_signal10.789428
Spike_AFFX-r2-P1-cre_3_signal3382.928711
Spike_AFFX-r2-Bs-lys_3-5-ratio1.590262
Spike_AFFX-r2-Bs-dap_M_signal147.826645
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.132846
Spike_AFFX-r2-Ec-bioB_avg-signal53.517609
Spike_AFFX-r2-Bs-thr_avg-signal38.490139
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal534.669128
Spike_AFFX-r2-Bs-phe_5_signal27.816004
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal811.822632
RawQ3.227382
Spike_AFFX-r2-Bs-lys_5_signal19.965263
Signal(A)4.273852
%A32.016659
Signal(All)140.351044
Corner+Avg:300,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal197.713638
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal39.529572
Spike_AFFX-r2-Ec-bioD_avg-signal673.245850
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.142044
Spike_AFFX-r2-Bs-lys_avg-signal20.834898
Spike_AFFX-r2-P1-cre_avg-signal2939.027100
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.841298
Spike_AFFX-r2-Bs-thr_3_signal46.697552
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal31.157000
Spike_AFFX-r2-Bs-dap_3_signal212.844025
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.518365
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal169.487915
#M420
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal31.750006
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.166535
Spike_AFFX-r2-Bs-thr_M_signal46.878372
Signal(P)209.677887
Spike_AFFX-r2-Bs-phe_3-5-ratio1.421109
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14318,Count:9
Spike_AFFX-r2-P1-cre_5_signal2495.125488
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7303
Signal(M)16.154673
BackgroundAvg:81.19,Std:0.60,Min:79.7,Max:82.9
Spike_AFFX-r2-Ec-bioC_avg-signal183.600769
Spike_AFFX-r2-Bs-dap_avg-signal153.069214
Spike_AFFX-r2-Bs-dap_3-5-ratio2.160042
Spike_AFFX-r2-Ec-bioB_5_signal41.161057
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.380049
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team