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Experiment: bob1-3 vs WT with and without a heat shock

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-570

BOB1 is a non-canonical Arabidopsis small heat shock protein. This experiment contains four samples: WT (Col-O) and bob1-3 4 day old seedlings grown at 22 degrees Celsius with or without a 75 minute 37 degree Celsius heat shock.

About the Experimenter

Name:Dr Nick Kaplinsky
Head of Lab Name:Dr Nick Kaplinsky
Lab:
Address:Department of Biology, Swarthmore College
500 College Ave, Swarthmore, Pennsylvania, 19081, UNITED STATES
Postcode:
Country:
 
Telephone Number: 1.610.328.8039

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:4
 
Experimental Parameters:
parameterchange_temperature
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Kaplinsky: bob1-3 vs WT with and without a heat shock

Slide: Kaplinsky_570-1_Col-RT_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 ("Kaplinsky_570-1_Col-RT_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: Kaplinsky_570-1_Col-RT_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code:
Genetic Background: Col
Age: 4 days
Growth Conditions:
Stratification2 d, 4°C
ProtocolPlants were grown for four days under continuous light on a shaker at 22 degrees celcius
Temperature22 °C
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent)4800 Lux
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:0.526358
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-ratio1.325805
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.275173
Spike_AFFX-r2-Bs-dap_5_signal153.090958
NoiseAvg:2.90,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_signal55.610626
#P13773
Spike_AFFX-r2-Bs-phe_M_signal105.500061
Corner-Avg:21279,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal124.257355
Spike_AFFX-r2-Ec-bioB_3_signal114.045395
Spike_AFFX-r2-Bs-lys_M_signal34.051796
Spike_AFFX-r2-P1-cre_3_signal5353.584473
Spike_AFFX-r2-Bs-lys_3-5-ratio1.752739
Spike_AFFX-r2-Bs-dap_M_signal451.068359
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.937101
Spike_AFFX-r2-Ec-bioB_avg-signal109.246002
Spike_AFFX-r2-Bs-thr_avg-signal133.374710
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal976.421326
Spike_AFFX-r2-Bs-phe_5_signal107.779259
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1709.554199
RawQ2.509935
Spike_AFFX-r2-Bs-lys_5_signal64.580124
Signal(A)4.705407
%A37.470409
Signal(All)151.866928
Corner+Avg:324,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal324.802887
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal155.359680
Spike_AFFX-r2-Ec-bioD_avg-signal1342.987793
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.381413
Spike_AFFX-r2-Bs-lys_avg-signal70.608009
Spike_AFFX-r2-P1-cre_avg-signal4695.785645
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.148181
Spike_AFFX-r2-Bs-thr_3_signal218.944656
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal122.879669
Spike_AFFX-r2-Bs-dap_3_signal717.604492
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.750837
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal338.105286
#M490
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal113.192116
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.960656
Spike_AFFX-r2-Bs-thr_M_signal125.568832
Signal(P)247.991104
Spike_AFFX-r2-Bs-phe_3-5-ratio1.441462
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:18684,Count:9
Spike_AFFX-r2-P1-cre_5_signal4037.986816
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8547
Signal(M)16.910540
BackgroundAvg:57.51,Std:0.75,Min:56.0,Max:59.5
Spike_AFFX-r2-Ec-bioC_avg-signal331.454102
Spike_AFFX-r2-Bs-dap_avg-signal440.587921
Spike_AFFX-r2-Bs-dap_3-5-ratio4.687439
Spike_AFFX-r2-Ec-bioB_5_signal89.435249
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.526358
NF1.000000
HZ4
Tau0.015000

Slide: Kaplinsky_570-2_Col-HS_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 ("Kaplinsky_570-2_Col-HS_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: Kaplinsky_570-2_Col-HS_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code:
Genetic Background: Col
Age: 4 days
Growth Conditions:
Stratification2 d, 4°C
ProtocolPlants were grown for four days under continuous light on a shaker at 22 degrees Celsius. At four days they were heat shocked at 37 degrees Celsius for 75 minutes.
Temperature22 °C
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent)4800 Lux
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: whole plant
Treatment Type: 75 minutes at 37 degrees Celsius in a lit shaking incubator
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:0.57723
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-ratio1.249691
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.995669
Spike_AFFX-r2-Bs-dap_5_signal254.984512
NoiseAvg:2.76,Std:0.08,Min:2.5,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_signal66.145645
#P13194
Spike_AFFX-r2-Bs-phe_M_signal124.899857
Corner-Avg:21996,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal188.617996
Spike_AFFX-r2-Ec-bioB_3_signal106.458885
Spike_AFFX-r2-Bs-lys_M_signal72.761971
Spike_AFFX-r2-P1-cre_3_signal6194.824707
Spike_AFFX-r2-Bs-lys_3-5-ratio1.294685
Spike_AFFX-r2-Bs-dap_M_signal624.536621
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.789409
Spike_AFFX-r2-Ec-bioB_avg-signal133.999588
Spike_AFFX-r2-Bs-thr_avg-signal172.908493
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1217.772461
Spike_AFFX-r2-Bs-phe_5_signal157.166763
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1818.006348
RawQ2.416529
Spike_AFFX-r2-Bs-lys_5_signal90.579414
Signal(A)4.838404
%A39.833405
Signal(All)163.735794
Corner+Avg:337,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal373.741211
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal172.778915
Spike_AFFX-r2-Ec-bioD_avg-signal1517.889404
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.843052
Spike_AFFX-r2-Bs-lys_avg-signal93.537743
Spike_AFFX-r2-P1-cre_avg-signal5575.955078
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.323542
Spike_AFFX-r2-Bs-thr_3_signal316.798553
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-signal151.615173
Spike_AFFX-r2-Bs-dap_3_signal930.260193
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.492895
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal408.501190
#M530
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal117.271835
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.914909
Spike_AFFX-r2-Bs-thr_M_signal135.781250
Signal(P)279.112915
Spike_AFFX-r2-Bs-phe_3-5-ratio1.099335
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:19412,Count:9
Spike_AFFX-r2-P1-cre_5_signal4957.085938
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9086
Signal(M)15.539691
BackgroundAvg:59.20,Std:0.28,Min:58.5,Max:59.9
Spike_AFFX-r2-Ec-bioC_avg-signal391.121216
Spike_AFFX-r2-Bs-dap_avg-signal603.260437
Spike_AFFX-r2-Bs-dap_3-5-ratio3.648301
Spike_AFFX-r2-Ec-bioB_5_signal106.921921
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.577230
NF1.000000
HZ4
Tau0.015000

Slide: Kaplinsky_570-3_bob-RT_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 ("Kaplinsky_570-3_bob-RT_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: Kaplinsky_570-3_bob-RT_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: bob1-3
Stock Code:
Genetic Background: Col
Age: 4 days
Growth Conditions:
Stratification2 d, 4°C
ProtocolPlants were grown for four days under continuous light on a shaker at 22 degrees celcius
Temperature22 °C
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent)4800 Lux
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation, At5g53400
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:0.496711
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-ratio1.256341
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.283210
Spike_AFFX-r2-Bs-dap_5_signal152.875504
NoiseAvg:2.78,Std:0.06,Min:2.6,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal41.725121
#P14225
Spike_AFFX-r2-Bs-phe_M_signal75.296265
Corner-Avg:20812,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal128.821533
Spike_AFFX-r2-Ec-bioB_3_signal122.600426
Spike_AFFX-r2-Bs-lys_M_signal30.667072
Spike_AFFX-r2-P1-cre_3_signal5384.840820
Spike_AFFX-r2-Bs-lys_3-5-ratio1.204159
Spike_AFFX-r2-Bs-dap_M_signal383.537964
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.140337
Spike_AFFX-r2-Ec-bioB_avg-signal115.654663
Spike_AFFX-r2-Bs-thr_avg-signal104.055183
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal989.243774
Spike_AFFX-r2-Bs-phe_5_signal104.820221
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1700.252563
RawQ2.406927
Spike_AFFX-r2-Bs-lys_5_signal60.781296
Signal(A)4.685764
%A35.440598
Signal(All)150.895462
Corner+Avg:330,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal327.537811
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal119.993347
Spike_AFFX-r2-Ec-bioD_avg-signal1344.748169
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.362999
Spike_AFFX-r2-Bs-lys_avg-signal54.879562
Spike_AFFX-r2-P1-cre_avg-signal4835.484863
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.196405
Spike_AFFX-r2-Bs-thr_3_signal172.756073
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-signal100.036613
Spike_AFFX-r2-Bs-dap_3_signal657.654175
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.718740
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal350.617615
#M501
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal73.190323
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.934174
Spike_AFFX-r2-Bs-thr_M_signal97.684364
Signal(P)238.787140
Spike_AFFX-r2-Bs-phe_3-5-ratio1.144754
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:18991,Count:9
Spike_AFFX-r2-P1-cre_5_signal4286.128906
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8084
Signal(M)14.568136
BackgroundAvg:55.91,Std:0.47,Min:54.7,Max:56.9
Spike_AFFX-r2-Ec-bioC_avg-signal339.077698
Spike_AFFX-r2-Bs-dap_avg-signal398.022552
Spike_AFFX-r2-Bs-dap_3-5-ratio4.301894
Spike_AFFX-r2-Ec-bioB_5_signal95.542007
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.496711
NF1.000000
HZ4
Tau0.015000

Slide: Kaplinsky_570-4_bob-HS_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 ("Kaplinsky_570-4_bob-HS_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: Kaplinsky_570-4_bob-HS_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: bob1-3
Stock Code:
Genetic Background: Col
Age: 4 days
Growth Conditions:
Stratification2 d, 4°C
ProtocolPlants were grown for four days under continuous light on a shaker at 22 degrees celcius
Temperature22 °C
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent)4800 Lux
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation, At5g53400
Tissue: whole plant
Treatment Type: 75 minutes at 37 degrees Celsius in a lit shaking incubator
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:0.594071
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-ratio1.174290
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.407758
Spike_AFFX-r2-Bs-dap_5_signal172.379364
NoiseAvg:2.56,Std:0.07,Min:2.4,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal68.038330
#P12672
Spike_AFFX-r2-Bs-phe_M_signal115.776436
Corner-Avg:19908,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal154.368851
Spike_AFFX-r2-Ec-bioB_3_signal85.929047
Spike_AFFX-r2-Bs-lys_M_signal73.945923
Spike_AFFX-r2-P1-cre_3_signal5516.777832
Spike_AFFX-r2-Bs-lys_3-5-ratio1.313897
Spike_AFFX-r2-Bs-dap_M_signal570.953430
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.862570
Spike_AFFX-r2-Ec-bioB_avg-signal100.445854
Spike_AFFX-r2-Bs-thr_avg-signal161.420273
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1035.987671
Spike_AFFX-r2-Bs-phe_5_signal149.091782
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1698.482788
RawQ2.455653
Spike_AFFX-r2-Bs-lys_5_signal96.256958
Signal(A)4.741146
%A42.152565
Signal(All)163.792236
Corner+Avg:308,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal326.237732
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal146.766464
Spike_AFFX-r2-Ec-bioD_avg-signal1367.235229
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P55.554581
Spike_AFFX-r2-Bs-lys_avg-signal98.891541
Spike_AFFX-r2-P1-cre_avg-signal5107.373047
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.292854
Spike_AFFX-r2-Bs-thr_3_signal262.802795
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-signal137.211563
Spike_AFFX-r2-Bs-dap_3_signal865.037781
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.639482
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal359.109314
#M523
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal126.471725
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.908464
Spike_AFFX-r2-Bs-thr_M_signal153.419708
Signal(P)290.576019
Spike_AFFX-r2-Bs-phe_3-5-ratio0.984403
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:19077,Count:9
Spike_AFFX-r2-P1-cre_5_signal4697.968750
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9615
Signal(M)15.937995
BackgroundAvg:56.82,Std:0.42,Min:55.7,Max:58.0
Spike_AFFX-r2-Ec-bioC_avg-signal342.673523
Spike_AFFX-r2-Bs-dap_avg-signal536.123535
Spike_AFFX-r2-Bs-dap_3-5-ratio5.018221
Spike_AFFX-r2-Ec-bioB_5_signal61.039650
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.594071
NF1.000000
HZ4
Tau0.015000


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