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Experiment: Understanding the affect of maternal environment on seed dormancy

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-594

Maternal environment is an important regulator of seed dormancy, but the mechanisms underlying the process are poorly understood. We have found that genes in the circadian clock control dormancy, in part through their regulation of the canonical photoperiod pathway known from research into flowering time control. In this experiment we compare the effects of altering seed maturation temperature or maternal photoperiod on dry seed transcriptomes, and the photoperiod-insenstive ft-1 mutant to wt type Ler. In this way we are identifying gene expression programmes which result from the seed's response to maternal environmental experience.

About the Experimenter

Name: Steven Penfield
Head of Lab Name: Steven Penfield
Lab:
Address:Department of Biology
University of York
Heslington
York
Postcode: Yo10 5DD
Country: UK
 
Telephone Number: 01904785889

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: genetic_modification_design; physiological_process_design
Number of Slides:12
 
Experimental Parameters:
parametergene_knock_out
parameterchange_temperature
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Penfield: Understanding the affect of maternal environment on seed dormancy

Slide: Penfield_2-1_Ler-20-degrees-long-day_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 ("Penfield_2-1_Ler-20-degrees-long-day_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: Penfield_2-1_Ler-20-degrees-long-day_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 9.7
Growth Conditions:
ProtocolPlants were grown in long 16h days at 20 degrees celcius under white fluorescent light at 80-100umol m-2 sec-2. Mature seed was collected from dehisced siliques.
Referencen/a
Protocol Urln/a
Soil ConstituentsLevington seed compost
Substrate Sterilising ProcedureIntercept
Plant SpacingI plant per P40 insert
waterdaily
Temperature20 °C average, 20 °C day, 20 °C night
Humidity80 % average, unknown % day, unknown % night
MediumNone. Applied: N/A
Lighting(Source: Fluorescent manufactured by unknown. Intensity: 100µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)9.70
Tissue: seeds
Additional Organism Information:
Sample DescriptionPlant had completed its lifecycle and was in the process of senescence.
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:0.892056
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-ratio1.400410
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.300844
Spike_AFFX-r2-Bs-dap_5_signal100.770081
NoiseAvg:1.63,Std:0.04,Min:1.5,Max:1.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal48.566071
#P12015
Spike_AFFX-r2-Bs-phe_M_signal77.438072
Corner-Avg:6818,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal197.956863
Spike_AFFX-r2-Ec-bioB_3_signal112.906265
Spike_AFFX-r2-Bs-lys_M_signal38.242691
Spike_AFFX-r2-P1-cre_3_signal7663.936035
Spike_AFFX-r2-Bs-lys_3-5-ratio1.341843
Spike_AFFX-r2-Bs-dap_M_signal360.644012
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.461205
Spike_AFFX-r2-Ec-bioB_avg-signal132.552582
Spike_AFFX-r2-Bs-thr_avg-signal271.109772
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1095.046997
Spike_AFFX-r2-Bs-phe_5_signal59.324337
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1665.376465
RawQ1.758403
Spike_AFFX-r2-Bs-lys_5_signal57.825424
Signal(A)4.499006
%A45.190704
Signal(All)158.358185
Corner+Avg:37,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal675.955994
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal97.428467
Spike_AFFX-r2-Ec-bioD_avg-signal1380.211670
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P52.674267
Spike_AFFX-r2-Bs-lys_avg-signal57.886913
Spike_AFFX-r2-P1-cre_avg-signal6568.286133
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.135029
Spike_AFFX-r2-Bs-thr_3_signal556.625671
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-signal78.063629
Spike_AFFX-r2-Bs-dap_3_signal526.507813
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.520826
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal527.411011
#M487
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal77.592613
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.281649
Spike_AFFX-r2-Bs-thr_M_signal208.137650
Signal(P)296.125122
Spike_AFFX-r2-Bs-phe_3-5-ratio1.642302
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4668,Count:9
Spike_AFFX-r2-P1-cre_5_signal5472.636719
Spike_AFFX-r2-Bs-phe_M_detectionP
#A10308
Signal(M)16.080379
BackgroundAvg:52.96,Std:0.14,Min:52.5,Max:53.3
Spike_AFFX-r2-Ec-bioC_avg-signal601.683472
Spike_AFFX-r2-Bs-dap_avg-signal329.307312
Spike_AFFX-r2-Bs-dap_3-5-ratio5.224843
Spike_AFFX-r2-Ec-bioB_5_signal86.794624
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.892056
NF1.000000
HZ4
Tau0.015000

Slide: Penfield_2-2_Ler-20-degrees-long-day_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 ("Penfield_2-2_Ler-20-degrees-long-day_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: Penfield_2-2_Ler-20-degrees-long-day_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 9.7
Growth Conditions:
ProtocolPlants were grown in long 16h days at 20 degrees celcius under white fluorescent light at 80-100umol m-2 sec-2. Mature seed was collected from dehisced siliques.
Referencen/a
Protocol Urln/a
Soil ConstituentsLevington seed compost
Substrate Sterilising ProcedureIntercept
Plant SpacingI plant per P40 insert
waterdaily
Temperature20 °C average, 20 °C day, 20 °C night
Humidity80 % average, unknown % day, unknown % night
MediumNone. Applied: N/A
Lighting(Source: Fluorescent manufactured by unknown. Intensity: 100µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)9.70
Tissue: seeds
Additional Organism Information:
Sample DescriptionPlant had completed its lifecycle and was in the process of senescence.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.210834
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-ratio1.186912
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.994415
Spike_AFFX-r2-Bs-dap_5_signal155.389832
NoiseAvg:2.00,Std:0.06,Min:1.8,Max:2.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal49.877422
#P11147
Spike_AFFX-r2-Bs-phe_M_signal83.191734
Corner-Avg:6393,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal223.100327
Spike_AFFX-r2-Ec-bioB_3_signal123.687981
Spike_AFFX-r2-Bs-lys_M_signal53.127823
Spike_AFFX-r2-P1-cre_3_signal8473.609375
Spike_AFFX-r2-Bs-lys_3-5-ratio1.561250
Spike_AFFX-r2-Bs-dap_M_signal401.735474
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio13.073089
Spike_AFFX-r2-Ec-bioB_avg-signal136.268494
Spike_AFFX-r2-Bs-thr_avg-signal307.933624
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1297.482788
Spike_AFFX-r2-Bs-phe_5_signal52.927830
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1960.720947
RawQ2.001298
Spike_AFFX-r2-Bs-lys_5_signal50.164482
Signal(A)6.787257
%A49.044277
Signal(All)161.404694
Corner+Avg:48,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal644.995178
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal68.946396
Spike_AFFX-r2-Ec-bioD_avg-signal1629.101807
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P48.868916
Spike_AFFX-r2-Bs-lys_avg-signal60.537201
Spike_AFFX-r2-P1-cre_avg-signal7806.406250
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.086804
Spike_AFFX-r2-Bs-thr_3_signal652.051941
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-signal68.355316
Spike_AFFX-r2-Bs-dap_3_signal407.187469
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.511173
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal582.894653
#M476
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal78.319298
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.106538
Spike_AFFX-r2-Bs-thr_M_signal221.871490
Signal(P)322.407410
Spike_AFFX-r2-Bs-phe_3-5-ratio1.302649
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:3691,Count:9
Spike_AFFX-r2-P1-cre_5_signal7139.203613
Spike_AFFX-r2-Bs-phe_M_detectionP
#A11187
Signal(M)24.866669
BackgroundAvg:57.37,Std:0.32,Min:56.7,Max:58.0
Spike_AFFX-r2-Ec-bioC_avg-signal613.944946
Spike_AFFX-r2-Bs-dap_avg-signal321.437592
Spike_AFFX-r2-Bs-dap_3-5-ratio2.620425
Spike_AFFX-r2-Ec-bioB_5_signal62.017178
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.210834
NF1.000000
HZ4
Tau0.015000

Slide: Penfield_2-3_Ler-20-degrees-long-day_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 ("Penfield_2-3_Ler-20-degrees-long-day_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: Penfield_2-3_Ler-20-degrees-long-day_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 9.7
Growth Conditions:
ProtocolPlants were grown in long 16h days at 20 degrees celcius under white fluorescent light at 80-100umol m-2 sec-2. Mature seed was collected from dehisced siliques.
Referencen/a
Protocol Urln/a
Soil ConstituentsLevington seed compost
Substrate Sterilising ProcedureIntercept
Plant SpacingI plant per P40 insert
waterdaily
Temperature20 °C average, 20 °C day, 20 °C night
Humidity80 % average, unknown % day, unknown % night
MediumNone. Applied: N/A
Lighting(Source: Fluorescent manufactured by unknown. Intensity: 100µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)9.70
Tissue: seeds
Additional Organism Information:
Sample DescriptionPlant had completed its lifecycle and was in the process of senescence.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.291338
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-ratio1.173685
Spike_AFFX-r2-Ec-bioB_3-5-ratio2.281212
Spike_AFFX-r2-Bs-dap_5_signal70.256638
NoiseAvg:1.77,Std:0.06,Min:1.6,Max:2.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal31.278021
#P11052
Spike_AFFX-r2-Bs-phe_M_signal82.080460
Corner-Avg:8878,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal297.246338
Spike_AFFX-r2-Ec-bioB_3_signal181.190674
Spike_AFFX-r2-Bs-lys_M_signal52.689255
Spike_AFFX-r2-P1-cre_3_signal7308.766113
Spike_AFFX-r2-Bs-lys_3-5-ratio1.249009
Spike_AFFX-r2-Bs-dap_M_signal288.480042
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.102641
Spike_AFFX-r2-Ec-bioB_avg-signal185.954788
Spike_AFFX-r2-Bs-thr_avg-signal141.980087
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1739.350464
Spike_AFFX-r2-Bs-phe_5_signal59.524536
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2381.914795
RawQ1.916491
Spike_AFFX-r2-Bs-lys_5_signal54.904633
Signal(A)6.059188
%A49.438843
Signal(All)162.915436
Corner+Avg:47,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal626.214966
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal80.502609
Spike_AFFX-r2-Ec-bioD_avg-signal2060.632568
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P48.452435
Spike_AFFX-r2-Bs-lys_avg-signal58.723423
Spike_AFFX-r2-P1-cre_avg-signal6767.979492
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.108724
Spike_AFFX-r2-Bs-thr_3_signal284.712585
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-signal74.035866
Spike_AFFX-r2-Bs-dap_3_signal517.313354
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.369428
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal504.278534
#M481
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal68.576385
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.241804
Spike_AFFX-r2-Bs-thr_M_signal109.949631
Signal(P)329.124512
Spike_AFFX-r2-Bs-phe_3-5-ratio1.352427
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6697,Count:9
Spike_AFFX-r2-P1-cre_5_signal6227.193359
Spike_AFFX-r2-Bs-phe_M_detectionP
#A11277
Signal(M)21.387495
BackgroundAvg:54.78,Std:0.50,Min:53.9,Max:56.3
Spike_AFFX-r2-Ec-bioC_avg-signal565.246765
Spike_AFFX-r2-Bs-dap_avg-signal292.016693
Spike_AFFX-r2-Bs-dap_3-5-ratio7.363195
Spike_AFFX-r2-Ec-bioB_5_signal79.427383
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.291338
NF1.000000
HZ4
Tau0.015000

Slide: Penfield_2-4_ft1-20-degrees-long-day_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 ("Penfield_2-4_ft1-20-degrees-long-day_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: Penfield_2-4_ft1-20-degrees-long-day_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Glabra
Stock Code: N65
Genetic Background: Ler
Age: 9.7
Growth Conditions:
ProtocolPlants were grown in long 16h days at 20 degrees celcius under white fluorescent light at 80-100umol m-2 sec-2. Mature seed was collected from dehisced siliques.
Referencen/a
Protocol Urln/a
Soil ConstituentsLevington seed compost
Substrate Sterilising ProcedureIntercept
Plant SpacingI plant per P40 insert
waterdaily
Temperature20 °C average, 20 °C day, 20 °C night
Humidity80 % average, unknown % day, unknown % night
MediumNone. Applied: N/A
Lighting(Source: Fluorescent manufactured by unknown. Intensity: 100µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)9.70
Genetic Variation: Single marker
Tissue: seeds
Additional Organism Information:
Sample DescriptionPlant had completed its lifecycle and was in the process of senescence.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.039723
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-ratio1.091459
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.488525
Spike_AFFX-r2-Bs-dap_5_signal19.861427
NoiseAvg:1.56,Std:0.04,Min:1.4,Max:1.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.358717
#P11701
Spike_AFFX-r2-Bs-phe_M_signal40.445686
Corner-Avg:8123,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal221.288177
Spike_AFFX-r2-Ec-bioB_3_signal154.814255
Spike_AFFX-r2-Bs-lys_M_signal38.043873
Spike_AFFX-r2-P1-cre_3_signal5915.713379
Spike_AFFX-r2-Bs-lys_3-5-ratio1.191807
Spike_AFFX-r2-Bs-dap_M_signal166.634155
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio37.343315
Spike_AFFX-r2-Ec-bioB_avg-signal160.035843
Spike_AFFX-r2-Bs-thr_avg-signal83.702774
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1267.705200
Spike_AFFX-r2-Bs-phe_5_signal26.233372
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1807.516113
RawQ1.937131
Spike_AFFX-r2-Bs-lys_5_signal51.147030
Signal(A)4.821939
%A46.834721
Signal(All)156.268723
Corner+Avg:44,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal469.651947
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal79.738998
Spike_AFFX-r2-Ec-bioD_avg-signal1537.610596
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P51.297676
Spike_AFFX-r2-Bs-lys_avg-signal50.049435
Spike_AFFX-r2-P1-cre_avg-signal5667.859375
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.867602
Spike_AFFX-r2-Bs-thr_3_signal200.112274
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-signal48.806019
Spike_AFFX-r2-Bs-dap_3_signal329.075165
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.425817
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal412.285797
#M426
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal60.957401
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.139142
Spike_AFFX-r2-Bs-thr_M_signal45.637337
Signal(P)299.539154
Spike_AFFX-r2-Bs-phe_3-5-ratio3.039602
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7191,Count:9
Spike_AFFX-r2-P1-cre_5_signal5420.004883
Spike_AFFX-r2-Bs-phe_M_detectionP
#A10683
Signal(M)18.942265
BackgroundAvg:55.38,Std:0.32,Min:54.3,Max:56.2
Spike_AFFX-r2-Ec-bioC_avg-signal440.968872
Spike_AFFX-r2-Bs-dap_avg-signal171.856918
Spike_AFFX-r2-Bs-dap_3-5-ratio16.568556
Spike_AFFX-r2-Ec-bioB_5_signal104.005142
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.039723
NF1.000000
HZ4
Tau0.015000

Slide: Penfield_2-5_ft1-20-degrees-long-day_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 ("Penfield_2-5_ft1-20-degrees-long-day_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: Penfield_2-5_ft1-20-degrees-long-day_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Glabra
Stock Code: N65
Genetic Background: Ler
Age: 9.7
Growth Conditions:
ProtocolPlants were grown in long 16h days at 20 degrees celcius under white fluorescent light at 80-100umol m-2 sec-2. Mature seed was collected from dehisced siliques.
Referencen/a
Protocol Urln/a
Soil ConstituentsLevington seed compost
Substrate Sterilising ProcedureIntercept
Plant SpacingI plant per P40 insert
waterdaily
Temperature20 °C average, 20 °C day, 20 °C night
Humidity80 % average, unknown % day, unknown % night
MediumNone. Applied: N/A
Lighting(Source: Fluorescent manufactured by unknown. Intensity: 100µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)9.70
Genetic Variation: Single marker
Tissue: seeds
Additional Organism Information:
Sample DescriptionPlant had completed its lifecycle and was in the process of senescence.
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:0.956691
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-ratio0.920647
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.411357
Spike_AFFX-r2-Bs-dap_5_signal245.024277
NoiseAvg:1.60,Std:0.05,Min:1.4,Max:1.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal55.870567
#P11273
Spike_AFFX-r2-Bs-phe_M_signal197.320724
Corner-Avg:8223,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal219.067657
Spike_AFFX-r2-Ec-bioB_3_signal145.710663
Spike_AFFX-r2-Bs-lys_M_signal94.038063
Spike_AFFX-r2-P1-cre_3_signal5131.380859
Spike_AFFX-r2-Bs-lys_3-5-ratio1.100654
Spike_AFFX-r2-Bs-dap_M_signal621.271240
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio18.653028
Spike_AFFX-r2-Ec-bioB_avg-signal156.006607
Spike_AFFX-r2-Bs-thr_avg-signal491.513519
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1225.344116
Spike_AFFX-r2-Bs-phe_5_signal102.188286
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2065.365234
RawQ1.833509
Spike_AFFX-r2-Bs-lys_5_signal136.102798
Signal(A)4.980191
%A48.509426
Signal(All)169.078400
Corner+Avg:46,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal566.408264
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal217.812210
Spike_AFFX-r2-Ec-bioD_avg-signal1645.354736
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P49.421307
Spike_AFFX-r2-Bs-lys_avg-signal126.647621
Spike_AFFX-r2-P1-cre_avg-signal5352.524414
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.069268
Spike_AFFX-r2-Bs-thr_3_signal1042.155273
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-signal172.440414
Spike_AFFX-r2-Bs-dap_3_signal1290.703857
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.685539
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal384.713287
#M472
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal149.802032
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.472287
Spike_AFFX-r2-Bs-thr_M_signal376.514709
Signal(P)336.473267
Spike_AFFX-r2-Bs-phe_3-5-ratio2.131479
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5239,Count:9
Spike_AFFX-r2-P1-cre_5_signal5573.667480
Spike_AFFX-r2-Bs-phe_M_detectionP
#A11065
Signal(M)18.027981
BackgroundAvg:52.51,Std:0.45,Min:51.0,Max:53.4
Spike_AFFX-r2-Ec-bioC_avg-signal475.560791
Spike_AFFX-r2-Bs-dap_avg-signal718.999756
Spike_AFFX-r2-Bs-dap_3-5-ratio5.267657
Spike_AFFX-r2-Ec-bioB_5_signal103.241508
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.956691
NF1.000000
HZ4
Tau0.015000

Slide: Penfield_2-6_ft1-20-degrees-long-day_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 ("Penfield_2-6_ft1-20-degrees-long-day_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: Penfield_2-6_ft1-20-degrees-long-day_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Glabra
Stock Code: N65
Genetic Background: Ler
Age: 9.7
Growth Conditions:
ProtocolPlants were grown in long 16h days at 20 degrees celcius under white fluorescent light at 80-100umol m-2 sec-2. Mature seed was collected from dehisced siliques.
Referencen/a
Protocol Urln/a
Soil ConstituentsLevington seed compost
Substrate Sterilising ProcedureIntercept
Plant SpacingI plant per P40 insert
waterdaily
Temperature20 °C average, 20 °C day, 20 °C night
Humidity80 % average, unknown % day, unknown % night
MediumNone. Applied: N/A
Lighting(Source: Fluorescent manufactured by unknown. Intensity: 100µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)9.70
Genetic Variation: Single marker
Tissue: seeds
Additional Organism Information:
Sample DescriptionPlant had completed its lifecycle and was in the process of senescence.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.625438
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-ratio1.067907
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.571942
Spike_AFFX-r2-Bs-dap_5_signal60.896965
NoiseAvg:1.37,Std:0.03,Min:1.3,Max:1.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal9.483309
#P11130
Spike_AFFX-r2-Bs-phe_M_signal58.151398
Corner-Avg:7108,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal322.622314
Spike_AFFX-r2-Ec-bioB_3_signal210.072098
Spike_AFFX-r2-Bs-lys_M_signal32.022892
Spike_AFFX-r2-P1-cre_3_signal7778.700195
Spike_AFFX-r2-Bs-lys_3-5-ratio1.248161
Spike_AFFX-r2-Bs-dap_M_signal223.646973
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio17.186605
Spike_AFFX-r2-Ec-bioB_avg-signal222.111008
Spike_AFFX-r2-Bs-thr_avg-signal79.594780
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1690.766357
Spike_AFFX-r2-Bs-phe_5_signal45.597813
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2347.842773
RawQ1.544865
Spike_AFFX-r2-Bs-lys_5_signal44.678936
Signal(A)5.944591
%A49.267864
Signal(All)162.804688
Corner+Avg:43,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal641.940674
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal62.276398
Spike_AFFX-r2-Ec-bioD_avg-signal2019.304565
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P48.794388
Spike_AFFX-r2-Bs-lys_avg-signal44.156113
Spike_AFFX-r2-P1-cre_avg-signal7531.378906
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.937747
Spike_AFFX-r2-Bs-thr_3_signal162.985886
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-signal55.341869
Spike_AFFX-r2-Bs-dap_3_signal347.424438
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.388626
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal493.979156
#M442
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal55.766514
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.299530
Spike_AFFX-r2-Bs-thr_M_signal66.315147
Signal(P)326.716766
Spike_AFFX-r2-Bs-phe_3-5-ratio1.365776
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6340,Count:9
Spike_AFFX-r2-P1-cre_5_signal7284.058105
Spike_AFFX-r2-Bs-phe_M_detectionP
#A11238
Signal(M)23.556698
BackgroundAvg:49.57,Std:0.18,Min:48.9,Max:50.1
Spike_AFFX-r2-Ec-bioC_avg-signal567.959900
Spike_AFFX-r2-Bs-dap_avg-signal210.656128
Spike_AFFX-r2-Bs-dap_3-5-ratio5.705119
Spike_AFFX-r2-Ec-bioB_5_signal133.638596
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.625438
NF1.000000
HZ4
Tau0.015000

Slide: Penfield_2-7_Ler-20-degrees-short-day_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 ("Penfield_2-7_Ler-20-degrees-short-day_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: Penfield_2-7_Ler-20-degrees-short-day_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 9.7
Growth Conditions:
ProtocolPlants were grown in short 8h days at 20 degrees celcius under white fluorescent light at 80-100umol m-2 sec-2. Mature seed was collected from dehisced siliques.
Referencen/a
Protocol Urln/a
Soil ConstituentsLevington seed compost
Substrate Sterilising ProcedureIntercept
Plant SpacingI plant per P40 insert
waterdaily
Temperature20 °C average, 20 °C day, 20 °C night
Humidity80 % average, unknown % day, unknown % night
MediumNone. Applied: N/A
Lighting(Source: Fluorescent manufactured by unknown. Intensity: 100µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)9.70
Tissue: seeds
Additional Organism Information:
Sample DescriptionPlant had completed its lifecycle and was in the process of senescence.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.148764
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-ratio0.950286
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.492904
Spike_AFFX-r2-Bs-dap_5_signal240.724564
NoiseAvg:1.76,Std:0.04,Min:1.7,Max:1.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal31.394310
#P11065
Spike_AFFX-r2-Bs-phe_M_signal163.327606
Corner-Avg:14503,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal267.502441
Spike_AFFX-r2-Ec-bioB_3_signal188.475128
Spike_AFFX-r2-Bs-lys_M_signal127.499565
Spike_AFFX-r2-P1-cre_3_signal6810.199707
Spike_AFFX-r2-Bs-lys_3-5-ratio2.028656
Spike_AFFX-r2-Bs-dap_M_signal778.485107
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio22.109241
Spike_AFFX-r2-Ec-bioB_avg-signal194.074951
Spike_AFFX-r2-Bs-thr_avg-signal318.156586
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1548.283203
Spike_AFFX-r2-Bs-phe_5_signal77.599968
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2228.951416
RawQ1.838847
Spike_AFFX-r2-Bs-lys_5_signal102.881561
Signal(A)6.267934
%A49.175800
Signal(All)169.098465
Corner+Avg:71,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal599.919983
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal237.547104
Spike_AFFX-r2-Ec-bioD_avg-signal1888.617310
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P48.509426
Spike_AFFX-r2-Bs-lys_avg-signal146.364151
Spike_AFFX-r2-P1-cre_avg-signal6988.336914
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.314774
Spike_AFFX-r2-Bs-thr_3_signal694.104370
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-signal159.491562
Spike_AFFX-r2-Bs-dap_3_signal983.555115
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.439628
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal503.243500
#M528
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal208.711334
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.192107
Spike_AFFX-r2-Bs-thr_M_signal228.971085
Signal(P)341.170593
Spike_AFFX-r2-Bs-phe_3-5-ratio3.061175
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12293,Count:9
Spike_AFFX-r2-P1-cre_5_signal7166.474121
Spike_AFFX-r2-Bs-phe_M_detectionP
#A11217
Signal(M)22.303314
BackgroundAvg:53.74,Std:0.18,Min:53.3,Max:54.1
Spike_AFFX-r2-Ec-bioC_avg-signal551.581726
Spike_AFFX-r2-Bs-dap_avg-signal667.588318
Spike_AFFX-r2-Bs-dap_3-5-ratio4.085811
Spike_AFFX-r2-Ec-bioB_5_signal126.247299
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.148764
NF1.000000
HZ4
Tau0.015000

Slide: Penfield_2-8_Ler-20-degrees-short-day_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 ("Penfield_2-8_Ler-20-degrees-short-day_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: Penfield_2-8_Ler-20-degrees-short-day_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 9.7
Growth Conditions:
ProtocolPlants were grown in short 8h days at 20 degrees celcius under white fluorescent light at 80-100umol m-2 sec-2. Mature seed was collected from dehisced siliques.
Referencen/a
Protocol Urln/a
Soil ConstituentsLevington seed compost
Substrate Sterilising ProcedureIntercept
Plant SpacingI plant per P40 insert
waterdaily
Temperature20 °C average, 20 °C day, 20 °C night
Humidity80 % average, unknown % day, unknown % night
MediumNone. Applied: N/A
Lighting(Source: Fluorescent manufactured by unknown. Intensity: 100µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)9.70
Tissue: seeds
Additional Organism Information:
Sample DescriptionPlant had completed its lifecycle and was in the process of senescence.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.000733
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-ratio1.271588
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.571109
Spike_AFFX-r2-Bs-dap_5_signal287.147339
NoiseAvg:1.83,Std:0.07,Min:1.7,Max:2.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal60.354153
#P11254
Spike_AFFX-r2-Bs-phe_M_signal148.538925
Corner-Avg:13911,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal265.200592
Spike_AFFX-r2-Ec-bioB_3_signal147.993164
Spike_AFFX-r2-Bs-lys_M_signal93.809601
Spike_AFFX-r2-P1-cre_3_signal8086.929688
Spike_AFFX-r2-Bs-lys_3-5-ratio0.951431
Spike_AFFX-r2-Bs-dap_M_signal910.216187
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio13.109812
Spike_AFFX-r2-Ec-bioB_avg-signal169.130127
Spike_AFFX-r2-Bs-thr_avg-signal358.784027
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1638.469116
Spike_AFFX-r2-Bs-phe_5_signal108.799782
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2374.189697
RawQ2.055705
Spike_AFFX-r2-Bs-lys_5_signal106.940834
Signal(A)5.188883
%A48.706707
Signal(All)168.559631
Corner+Avg:67,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal573.100037
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal246.551758
Spike_AFFX-r2-Ec-bioD_avg-signal2006.329346
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P49.338009
Spike_AFFX-r2-Bs-lys_avg-signal100.832436
Spike_AFFX-r2-P1-cre_avg-signal7223.320313
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.955283
Spike_AFFX-r2-Bs-thr_3_signal791.231567
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-signal167.963486
Spike_AFFX-r2-Bs-dap_3_signal903.075928
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.449029
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal563.792236
#M446
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal101.746872
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.016509
Spike_AFFX-r2-Bs-thr_M_signal224.766296
Signal(P)335.766418
Spike_AFFX-r2-Bs-phe_3-5-ratio2.266105
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9792,Count:9
Spike_AFFX-r2-P1-cre_5_signal6359.710449
Spike_AFFX-r2-Bs-phe_M_detectionP
#A11110
Signal(M)19.016657
BackgroundAvg:55.15,Std:0.29,Min:54.3,Max:55.7
Spike_AFFX-r2-Ec-bioC_avg-signal568.446167
Spike_AFFX-r2-Bs-dap_avg-signal700.146484
Spike_AFFX-r2-Bs-dap_3-5-ratio3.144991
Spike_AFFX-r2-Ec-bioB_5_signal94.196640
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.000733
NF1.000000
HZ4
Tau0.015000

Slide: Penfield_2-9_Ler-20-degrees-short-day_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 ("Penfield_2-9_Ler-20-degrees-short-day_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: Penfield_2-9_Ler-20-degrees-short-day_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 9.7
Growth Conditions:
ProtocolPlants were grown in short 8h days at 20 degrees celcius under white fluorescent light at 80-100umol m-2 sec-2. Mature seed was collected from dehisced siliques.
Referencen/a
Protocol Urln/a
Soil ConstituentsLevington seed compost
Substrate Sterilising ProcedureIntercept
Plant SpacingI plant per P40 insert
waterdaily
Temperature20 °C average, 20 °C day, 20 °C night
Humidity80 % average, unknown % day, unknown % night
MediumNone. Applied: N/A
Lighting(Source: Fluorescent manufactured by unknown. Intensity: 100µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)9.70
Tissue: seeds
Additional Organism Information:
Sample DescriptionPlant had completed its lifecycle and was in the process of senescence.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.282215
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-ratio0.900462
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.483034
Spike_AFFX-r2-Bs-dap_5_signal248.429108
NoiseAvg:1.67,Std:0.04,Min:1.5,Max:1.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal71.628853
#P10971
Spike_AFFX-r2-Bs-phe_M_signal113.749039
Corner-Avg:7916,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal253.810501
Spike_AFFX-r2-Ec-bioB_3_signal182.651337
Spike_AFFX-r2-Bs-lys_M_signal63.056488
Spike_AFFX-r2-P1-cre_3_signal6123.904297
Spike_AFFX-r2-Bs-lys_3-5-ratio2.279709
Spike_AFFX-r2-Bs-dap_M_signal595.546997
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio12.852674
Spike_AFFX-r2-Ec-bioB_avg-signal186.540817
Spike_AFFX-r2-Bs-thr_avg-signal429.590973
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1649.823120
Spike_AFFX-r2-Bs-phe_5_signal84.581062
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2243.406006
RawQ1.866135
Spike_AFFX-r2-Bs-lys_5_signal90.612457
Signal(A)5.982775
%A49.820255
Signal(All)172.140808
Corner+Avg:44,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal794.643738
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal159.742035
Spike_AFFX-r2-Ec-bioD_avg-signal1946.614502
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P48.097324
Spike_AFFX-r2-Bs-lys_avg-signal120.079651
Spike_AFFX-r2-P1-cre_avg-signal6462.376953
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.082420
Spike_AFFX-r2-Bs-thr_3_signal920.622314
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-signal119.357384
Spike_AFFX-r2-Bs-dap_3_signal799.617981
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.359786
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal582.413208
#M475
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal206.570007
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.364399
Spike_AFFX-r2-Bs-thr_M_signal296.521790
Signal(P)350.780823
Spike_AFFX-r2-Bs-phe_3-5-ratio1.888626
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5929,Count:9
Spike_AFFX-r2-P1-cre_5_signal6800.849609
Spike_AFFX-r2-Bs-phe_M_detectionP
#A11364
Signal(M)21.320539
BackgroundAvg:51.78,Std:0.18,Min:51.3,Max:52.4
Spike_AFFX-r2-Ec-bioC_avg-signal688.528442
Spike_AFFX-r2-Bs-dap_avg-signal547.864685
Spike_AFFX-r2-Bs-dap_3-5-ratio3.218697
Spike_AFFX-r2-Ec-bioB_5_signal123.160599
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.282215
NF1.000000
HZ4
Tau0.015000

Slide: Penfield_2-10_Ler-10-degrees-long-day_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 ("Penfield_2-10_Ler-10-degrees-long-day_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: Penfield_2-10_Ler-10-degrees-long-day_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 9.7
Growth Conditions:
ProtocolPlants were grown to flowering in long 16h days at 20 degrees celcius under white fluorescent light at 80-100umol m-2 sec-2. After flowering the temperature was changed to 10 degrees celcius until maturity, other parameters were maintained. Mature seed was collected from dehisced siliques.
Referencen/a
Protocol Urln/a
Soil ConstituentsLevington seed compost
Substrate Sterilising ProcedureIntercept
Plant SpacingI plant per P40 insert
waterdaily
Temperature10 °C average, 10 °C day, 10 °C night
Humidity80 % average, unknown % day, unknown % night
MediumNone. Applied: N/A
Lighting(Source: Fluorescent manufactured by unknown. Intensity: 100µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)9.70
Tissue: seeds
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.481867
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-ratio0.901857
Spike_AFFX-r2-Ec-bioB_3-5-ratio2.344979
Spike_AFFX-r2-Bs-dap_5_signal567.963379
NoiseAvg:1.80,Std:0.08,Min:1.6,Max:2.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal134.457230
#P9847
Spike_AFFX-r2-Bs-phe_M_signal375.439453
Corner-Avg:15326,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal437.855377
Spike_AFFX-r2-Ec-bioB_3_signal260.103180
Spike_AFFX-r2-Bs-lys_M_signal283.873199
Spike_AFFX-r2-P1-cre_3_signal10240.172852
Spike_AFFX-r2-Bs-lys_3-5-ratio0.648252
Spike_AFFX-r2-Bs-dap_M_signal1606.687134
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.496686
Spike_AFFX-r2-Ec-bioB_avg-signal269.625916
Spike_AFFX-r2-Bs-thr_avg-signal623.698303
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal2380.706543
Spike_AFFX-r2-Bs-phe_5_signal277.839752
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal3561.579102
RawQ2.244879
Spike_AFFX-r2-Bs-lys_5_signal217.838943
Signal(A)8.199146
%A54.436649
Signal(All)192.820923
Corner+Avg:65,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal894.071594
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal490.291107
Spike_AFFX-r2-Ec-bioD_avg-signal2971.142822
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P43.169662
Spike_AFFX-r2-Bs-lys_avg-signal214.308899
Spike_AFFX-r2-P1-cre_avg-signal10797.355469
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.393687
Spike_AFFX-r2-Bs-thr_3_signal1276.898071
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-signal381.190094
Spike_AFFX-r2-Bs-dap_3_signal2408.913330
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.496018
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal741.626709
#M546
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal141.214539
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.205555
Spike_AFFX-r2-Bs-thr_M_signal459.739502
Signal(P)434.680145
Spike_AFFX-r2-Bs-phe_3-5-ratio1.764654
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12477,Count:9
Spike_AFFX-r2-P1-cre_5_signal11354.537109
Spike_AFFX-r2-Bs-phe_M_detectionP
#A12417
Signal(M)29.562252
BackgroundAvg:58.37,Std:0.32,Min:57.3,Max:59.1
Spike_AFFX-r2-Ec-bioC_avg-signal817.849121
Spike_AFFX-r2-Bs-dap_avg-signal1527.854614
Spike_AFFX-r2-Bs-dap_3-5-ratio4.241318
Spike_AFFX-r2-Ec-bioB_5_signal110.919189
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.481867
NF1.000000
HZ4
Tau0.015000

Slide: Penfield_2-11_Ler-10-degrees-long-day_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 ("Penfield_2-11_Ler-10-degrees-long-day_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: Penfield_2-11_Ler-10-degrees-long-day_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 9.7
Growth Conditions:
ProtocolPlants were grown to flowering in long 16h days at 20 degrees celcius under white fluorescent light at 80-100umol m-2 sec-2. After flowering the temperature was changed to 10 degrees celcius until maturity, other parameters were maintained. Mature seed was collected from dehisced siliques.
Referencen/a
Protocol Urln/a
Soil ConstituentsLevington seed compost
Substrate Sterilising ProcedureIntercept
Plant SpacingI plant per P40 insert
waterdaily
Temperature10 °C average, 10 °C day, 10 °C night
Humidity80 % average, unknown % day, unknown % night
MediumNone. Applied: N/A
Lighting(Source: Fluorescent manufactured by unknown. Intensity: 100µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)9.70
Tissue: seeds
Additional Organism Information:
Sample DescriptionPlant had completed its lifecycle and was in the process of senescence.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.308842
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-ratio1.260603
Spike_AFFX-r2-Ec-bioB_3-5-ratio3.018810
Spike_AFFX-r2-Bs-dap_5_signal436.697357
NoiseAvg:2.14,Std:0.07,Min:2.0,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal103.108543
#P10480
Spike_AFFX-r2-Bs-phe_M_signal229.517044
Corner-Avg:15994,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal455.290314
Spike_AFFX-r2-Ec-bioB_3_signal261.931641
Spike_AFFX-r2-Bs-lys_M_signal144.987427
Spike_AFFX-r2-P1-cre_3_signal11964.920898
Spike_AFFX-r2-Bs-lys_3-5-ratio1.065392
Spike_AFFX-r2-Bs-dap_M_signal1208.501343
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.862024
Spike_AFFX-r2-Ec-bioB_avg-signal267.996155
Spike_AFFX-r2-Bs-thr_avg-signal439.859253
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal2558.908936
Spike_AFFX-r2-Bs-phe_5_signal114.528709
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal3384.533203
RawQ2.140674
Spike_AFFX-r2-Bs-lys_5_signal118.698654
Signal(A)7.650971
%A51.757999
Signal(All)184.763794
Corner+Avg:71,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal915.633301
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal285.047882
Spike_AFFX-r2-Ec-bioD_avg-signal2971.721191
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P45.944759
Spike_AFFX-r2-Bs-lys_avg-signal130.048889
Spike_AFFX-r2-P1-cre_avg-signal10728.173828
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.297238
Spike_AFFX-r2-Bs-thr_3_signal913.750427
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-signal209.697876
Spike_AFFX-r2-Bs-dap_3_signal1257.416382
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.322647
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal676.530029
#M524
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal126.460556
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.353426
Spike_AFFX-r2-Bs-thr_M_signal302.718872
Signal(P)392.191589
Spike_AFFX-r2-Bs-phe_3-5-ratio2.488877
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11262,Count:9
Spike_AFFX-r2-P1-cre_5_signal9491.426758
Spike_AFFX-r2-Bs-phe_M_detectionP
#A11806
Signal(M)26.654789
BackgroundAvg:57.84,Std:0.53,Min:56.4,Max:59.3
Spike_AFFX-r2-Ec-bioC_avg-signal796.081665
Spike_AFFX-r2-Bs-dap_avg-signal967.538330
Spike_AFFX-r2-Bs-dap_3-5-ratio2.879377
Spike_AFFX-r2-Ec-bioB_5_signal86.766525
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.308842
NF1.000000
HZ4
Tau0.015000

Slide: Penfield_2-12_Ler-10-degrees-long-day_Rep3_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 ("Penfield_2-12_Ler-10-degrees-long-day_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: Penfield_2-12_Ler-10-degrees-long-day_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Landsberg erecta (Ler-0)
Stock Code: NW20
Age: 9.7
Growth Conditions:
ProtocolPlants were grown to flowering in long 16h days at 20 degrees celcius under white fluorescent light at 80-100umol m-2 sec-2. After flowering the temperature was changed to 10 degrees celcius until maturity, other parameters were maintained. Mature seed was collected from dehisced siliques.
Referencen/a
Protocol Urln/a
Soil ConstituentsLevington seed compost
Substrate Sterilising ProcedureIntercept
Plant SpacingI plant per P40 insert
waterdaily
Temperature10 °C average, 10 °C day, 10 °C night
Humidity80 % average, unknown % day, unknown % night
MediumNone. Applied: N/A
Lighting(Source: Fluorescent manufactured by unknown. Intensity: 100µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)9.70
Tissue: seeds
Additional Organism Information:
Sample DescriptionPlant had completed its lifecycle and was in the process of senescence.
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.354608
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-ratio1.041053
Spike_AFFX-r2-Ec-bioB_3-5-ratio2.395373
Spike_AFFX-r2-Bs-dap_5_signal507.007690
NoiseAvg:2.00,Std:0.15,Min:1.7,Max:2.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal128.129150
#P10015
Spike_AFFX-r2-Bs-phe_M_signal373.632019
Corner-Avg:14527,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal421.314819
Spike_AFFX-r2-Ec-bioB_3_signal226.219223
Spike_AFFX-r2-Bs-lys_M_signal258.423218
Spike_AFFX-r2-P1-cre_3_signal10019.677734
Spike_AFFX-r2-Bs-lys_3-5-ratio0.673882
Spike_AFFX-r2-Bs-dap_M_signal1376.522339
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio13.635126
Spike_AFFX-r2-Ec-bioB_avg-signal247.324707
Spike_AFFX-r2-Bs-thr_avg-signal826.288818
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal2290.551270
Spike_AFFX-r2-Bs-phe_5_signal154.332916
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2993.867188
RawQ2.101744
Spike_AFFX-r2-Bs-lys_5_signal222.690247
Signal(A)7.315539
%A53.888645
Signal(All)189.682495
Corner+Avg:72,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal777.488525
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal472.960968
Spike_AFFX-r2-Ec-bioD_avg-signal2642.209229
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P43.906181
Spike_AFFX-r2-Bs-lys_avg-signal210.393478
Spike_AFFX-r2-P1-cre_avg-signal9822.119141
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.205173
Spike_AFFX-r2-Bs-thr_3_signal1747.057129
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-signal333.641968
Spike_AFFX-r2-Bs-dap_3_signal2008.921265
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.307051
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal741.323059
#M503
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal150.066986
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.048785
Spike_AFFX-r2-Bs-thr_M_signal603.680176
Signal(P)421.773834
Spike_AFFX-r2-Bs-phe_3-5-ratio3.064550
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9144,Count:9
Spike_AFFX-r2-P1-cre_5_signal9624.560547
Spike_AFFX-r2-Bs-phe_M_detectionP
#A12292
Signal(M)25.189226
BackgroundAvg:58.58,Std:0.49,Min:57.7,Max:59.7
Spike_AFFX-r2-Ec-bioC_avg-signal759.405762
Spike_AFFX-r2-Bs-dap_avg-signal1297.483765
Spike_AFFX-r2-Bs-dap_3-5-ratio3.962309
Spike_AFFX-r2-Ec-bioB_5_signal94.440071
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.354608
NF1.000000
HZ4
Tau0.015000


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