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Experiment: Transcript profiling of PPDK and PCK mutant seedlings

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-534

This experiment aims to assess effects on transcriptional profiles of knocking out genes encoding two enzymes of C4 photosynthesis, PPDK (At4g15530) and PCK (At4g37870), both individually and in combination in Arabidopsis seedlings. This is to be achieved using T-DNA insert lines N616158 and N532133 and a double mutant created by a cross between these two lines. Each will be compared to the wild type Col-0. Tissue has been collected from seedlings which have been grown in the dark at 24oC for two days after a 30 min light pulse. Three biological replicates have been used for both Col-0 and each line.

About the Experimenter

Name:Miss Holly Astley
Head of Lab Name: Julian Hibberd
Lab:
Address:Department of Plant Sciences, University of Cambridge
Downing street, Cambridge, Cambridgeshire, CB2 3EA, UNITED KINGDOM
Postcode:
Country:
 
Telephone Number: 01223330220

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
Number of Slides:12
 
Experimental Parameters:
parametergene_knock_out
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Astley: Transcript profiling of PPDK and PCK mutant seedlings

Slide: Astley_534-1_Col-0_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 ("Astley_534-1_Col-0_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: Astley_534-1_Col-0_Rep1 _ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 2 days old
Growth Conditions:
StratificationAfter sowing, seed was incubated at 4 oC in the dark for 3 days.
SterilisationSeed was rinsed briefly in 70 % (v/v) ethanol (Fisher Scientific) before being soaked in 10 % (v/v) sodium hypochlorite (Fisher Scientific) for 20 min. Seed was then rinsed three times in sterile water.
ProtocolSterilised seed was sown under sterile conditions onto 20 um nylon mesh (Normesh Limited) over 10 ml medium in 60 ml containers (Sterilin) with loosely fitted lids sealed with Micropore surgical tape (3M). Seed was stratified for 3 days before being subjected to a 30 min light pulse at 200 umol m-2 s-1 photosynthetically active radiation and 24 oC. Seed was then maintined in the dark at 24 oC for 2 days before tissue was harvested.
Percentage Agrose0.8
Substrate Sterilising ProcedureMedia was sterilised by autoclaving for 1.5 h.
Plant SpacingApprox. 100 per square cm
Temperature24 °C average, 24 °C day, 24 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by GE Healthcare. Intensity: 200µEinsteins. Wavelength: White)10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
Additional Organism Information:
Sample Description2 day old whole etiolated seedlings
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:0.574212
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-ratio1.281684
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.820053
Spike_AFFX-r2-Bs-dap_5_signal130.938309
NoiseAvg:2.43,Std:0.09,Min:2.2,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal60.026295
#P14763
Spike_AFFX-r2-Bs-phe_M_signal80.999092
Corner-Avg:6958,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal76.276192
Spike_AFFX-r2-Ec-bioB_3_signal42.600739
Spike_AFFX-r2-Bs-lys_M_signal35.825672
Spike_AFFX-r2-P1-cre_3_signal3503.488037
Spike_AFFX-r2-Bs-lys_3-5-ratio1.410346
Spike_AFFX-r2-Bs-dap_M_signal300.996033
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.325855
Spike_AFFX-r2-Ec-bioB_avg-signal56.941906
Spike_AFFX-r2-Bs-thr_avg-signal176.329773
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal600.758545
Spike_AFFX-r2-Bs-phe_5_signal85.693535
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal887.351929
RawQ2.194164
Spike_AFFX-r2-Bs-lys_5_signal36.827877
Signal(A)3.811491
%A33.393250
Signal(All)137.759293
Corner+Avg:77,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal237.591080
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal85.957863
Spike_AFFX-r2-Ec-bioD_avg-signal744.055237
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.721611
Spike_AFFX-r2-Bs-lys_avg-signal41.531200
Spike_AFFX-r2-P1-cre_avg-signal3118.495605
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.885138
Spike_AFFX-r2-Bs-thr_3_signal319.691315
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-signal84.216827
Spike_AFFX-r2-Bs-dap_3_signal473.606995
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.477053
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal200.911774
#M430
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal51.940044
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.182564
Spike_AFFX-r2-Bs-thr_M_signal149.271713
Signal(P)210.455017
Spike_AFFX-r2-Bs-phe_3-5-ratio1.003085
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4329,Count:9
Spike_AFFX-r2-P1-cre_5_signal2733.503174
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7617
Signal(M)14.673762
BackgroundAvg:55.48,Std:0.27,Min:54.8,Max:56.4
Spike_AFFX-r2-Ec-bioC_avg-signal219.251434
Spike_AFFX-r2-Bs-dap_avg-signal301.847107
Spike_AFFX-r2-Bs-dap_3-5-ratio3.617024
Spike_AFFX-r2-Ec-bioB_5_signal51.948784
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.574212
NF1.000000
HZ4
Tau0.015000

Slide: Astley_534-2_ Col-0_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 ("Astley_534-2_ Col-0_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: Astley_534-2_ Col-0_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 2 days old
Growth Conditions:
StratificationAfter sowing, seed was incubated at 4 oC in the dark for 3 days.
SterilisationSeed was rinsed briefly in 70 % (v/v) ethanol (Fisher Scientific) before being soaked in 10 % (v/v) sodium hypochlorite (Fisher Scientific) for 20 min. Seed was then rinsed three times in sterile water.
ProtocolSterilised seed was sown under sterile conditions onto 20 um nylon mesh (Normesh Limited) over 10 ml medium in 60 ml containers (Sterilin) with loosely fitted lids sealed with Micropore surgical tape (3M). Seed was stratified for 3 days before being subjected to a 30 min light pulse at 200 umol m-2 s-1 photosynthetically active radiation and 24 oC. Seed was then maintined in the dark at 24 oC for 2 days before tissue was harvested.
Percentage Agrose0.8
Substrate Sterilising ProcedureMedia was sterilised by autoclaving for 1.5 h.
Plant SpacingApprox. 100 per square cm
Temperature24 °C average, 24 °C day, 24 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by GE Healthcare. Intensity: 200µEinsteins. Wavelength: White)10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
Additional Organism Information:
Sample Description2 day old whole etiolated seedlings
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:0.804745
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-ratio1.008866
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.128130
Spike_AFFX-r2-Bs-dap_5_signal122.110374
NoiseAvg:2.48,Std:0.07,Min:2.3,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal69.119690
#P13444
Spike_AFFX-r2-Bs-phe_M_signal99.935883
Corner-Avg:7694,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal92.751495
Spike_AFFX-r2-Ec-bioB_3_signal62.090130
Spike_AFFX-r2-Bs-lys_M_signal35.270561
Spike_AFFX-r2-P1-cre_3_signal3849.821289
Spike_AFFX-r2-Bs-lys_3-5-ratio1.479945
Spike_AFFX-r2-Bs-dap_M_signal418.223633
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.260540
Spike_AFFX-r2-Ec-bioB_avg-signal69.959900
Spike_AFFX-r2-Bs-thr_avg-signal265.216187
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal741.677795
Spike_AFFX-r2-Bs-phe_5_signal94.773216
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1266.525635
RawQ2.439850
Spike_AFFX-r2-Bs-lys_5_signal57.387081
Signal(A)5.688710
%A38.851379
Signal(All)147.148773
Corner+Avg:97,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal259.450165
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal129.342941
Spike_AFFX-r2-Ec-bioD_avg-signal1004.101685
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.939060
Spike_AFFX-r2-Bs-lys_avg-signal59.195789
Spike_AFFX-r2-P1-cre_avg-signal3832.905273
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.209557
Spike_AFFX-r2-Bs-thr_3_signal501.846252
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-signal108.017342
Spike_AFFX-r2-Bs-dap_3_signal549.561218
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.707649
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal297.482758
#M504
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal84.929733
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.872152
Spike_AFFX-r2-Bs-thr_M_signal224.682602
Signal(P)245.155029
Spike_AFFX-r2-Bs-phe_3-5-ratio1.364763
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4600,Count:9
Spike_AFFX-r2-P1-cre_5_signal3815.989014
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8862
Signal(M)20.210173
BackgroundAvg:61.89,Std:0.47,Min:60.5,Max:63.0
Spike_AFFX-r2-Ec-bioC_avg-signal278.466461
Spike_AFFX-r2-Bs-dap_avg-signal363.298431
Spike_AFFX-r2-Bs-dap_3-5-ratio4.500528
Spike_AFFX-r2-Ec-bioB_5_signal55.038074
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.804745
NF1.000000
HZ4
Tau0.015000

Slide: Astley_534-3_Col-0_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 ("Astley_534-3_Col-0_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: Astley_534-3_Col-0_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 2 days old
Growth Conditions:
StratificationAfter sowing, seed was incubated at 4 oC in the dark for 3 days.
SterilisationSeed was rinsed briefly in 70 % (v/v) ethanol (Fisher Scientific) before being soaked in 10 % (v/v) sodium hypochlorite (Fisher Scientific) for 20 min. Seed was then rinsed three times in sterile water.
ProtocolSterilised seed was sown under sterile conditions onto 20 um nylon mesh (Normesh Limited) over 10 ml medium in 60 ml containers (Sterilin) with loosely fitted lids sealed with Micropore surgical tape (3M). Seed was stratified for 3 days before being subjected to a 30 min light pulse at 200 umol m-2 s-1 photosynthetically active radiation and 24 oC. Seed was then maintined in the dark at 24 oC for 2 days before tissue was harvested.
Percentage Agrose0.8
Substrate Sterilising ProcedureMedia was sterilised by autoclaving for 1.5 h.
Plant SpacingApprox. 100 per square cm
Temperature24 °C average, 24 °C day, 24 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by GE Healthcare. Intensity: 200µEinsteins. Wavelength: White)10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Tissue: whole plant
Additional Organism Information:
Sample Description2 day old whole etiolated seedlings
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:0.975293
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-ratio1.009116
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.923918
Spike_AFFX-r2-Bs-dap_5_signal216.762711
NoiseAvg:1.85,Std:0.05,Min:1.8,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_signal107.152550
#P14393
Spike_AFFX-r2-Bs-phe_M_signal104.581604
Corner-Avg:6408,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal131.191833
Spike_AFFX-r2-Ec-bioB_3_signal91.090126
Spike_AFFX-r2-Bs-lys_M_signal52.457832
Spike_AFFX-r2-P1-cre_3_signal5083.080566
Spike_AFFX-r2-Bs-lys_3-5-ratio0.908283
Spike_AFFX-r2-Bs-dap_M_signal530.224670
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.849342
Spike_AFFX-r2-Ec-bioB_avg-signal106.957703
Spike_AFFX-r2-Bs-thr_avg-signal243.199265
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1031.695435
Spike_AFFX-r2-Bs-phe_5_signal134.769577
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1613.593384
RawQ1.903916
Spike_AFFX-r2-Bs-lys_5_signal67.056427
Signal(A)4.785598
%A34.958351
Signal(All)141.991714
Corner+Avg:72,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal423.273376
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal109.268623
Spike_AFFX-r2-Ec-bioD_avg-signal1322.644409
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.099518
Spike_AFFX-r2-Bs-lys_avg-signal60.140163
Spike_AFFX-r2-P1-cre_avg-signal5060.121094
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.942131
Spike_AFFX-r2-Bs-thr_3_signal412.466858
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-signal116.206604
Spike_AFFX-r2-Bs-dap_3_signal591.848694
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.564021
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal367.084930
#M443
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal60.906231
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.153067
Spike_AFFX-r2-Bs-thr_M_signal209.978409
Signal(P)221.858719
Spike_AFFX-r2-Bs-phe_3-5-ratio0.810781
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4838,Count:9
Spike_AFFX-r2-P1-cre_5_signal5037.161621
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7974
Signal(M)16.835733
BackgroundAvg:48.70,Std:0.47,Min:47.5,Max:50.2
Spike_AFFX-r2-Ec-bioC_avg-signal395.179138
Spike_AFFX-r2-Bs-dap_avg-signal446.278687
Spike_AFFX-r2-Bs-dap_3-5-ratio2.730399
Spike_AFFX-r2-Ec-bioB_5_signal98.591171
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.975293
NF1.000000
HZ4
Tau0.015000

Slide: Astley_534-4_PPDK-mutant_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 ("Astley_534-4_PPDK-mutant_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: Astley_534-4_PPDK-mutant_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_116158 (AO) (BT)
Stock Code: N616158
Genetic Background: Col-0 (Columbia, N60000)
Age: 2 days old
Growth Conditions:
StratificationAfter sowing, seed was incubated at 4 oC in the dark for 3 days.
SterilisationSeed was rinsed briefly in 70 % (v/v) ethanol (Fisher Scientific) before being soaked in 10 % (v/v) sodium hypochlorite (Fisher Scientific) for 20 min. Seed was then rinsed three times in sterile water.
ProtocolSterilised seed was sown under sterile conditions onto 20 um nylon mesh (Normesh Limited) over 10 ml medium in 60 ml containers (Sterilin) with loosely fitted lids sealed with Micropore surgical tape (3M). Seed was stratified for 3 days before being subjected to a 30 min light pulse at 200 umol m-2 s-1 photosynthetically active radiation and 24 oC. Seed was then maintined in the dark at 24 oC for 2 days before tissue was harvested.
Percentage Agrose0.8
Substrate Sterilising ProcedureMedia was sterilised by autoclaving for 1.5 h.
Plant SpacingApprox. 100 per square cm
Temperature24 °C average, 24 °C day, 24 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by GE Healthcare. Intensity: 200µEinsteins. Wavelength: White)10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Genetic Variation: T-DNA Insertion
Tissue: whole plant
Additional Organism Information:
Sample Description2 day old whole etiolated seedlings
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:0.521169
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-ratio1.141205
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.801086
Spike_AFFX-r2-Bs-dap_5_signal153.572144
NoiseAvg:2.44,Std:0.09,Min:2.2,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal64.528595
#P14527
Spike_AFFX-r2-Bs-phe_M_signal83.151283
Corner-Avg:7682,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal84.819466
Spike_AFFX-r2-Ec-bioB_3_signal52.870277
Spike_AFFX-r2-Bs-lys_M_signal38.683491
Spike_AFFX-r2-P1-cre_3_signal3701.367920
Spike_AFFX-r2-Bs-lys_3-5-ratio1.380847
Spike_AFFX-r2-Bs-dap_M_signal387.043457
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.803169
Spike_AFFX-r2-Ec-bioB_avg-signal67.895988
Spike_AFFX-r2-Bs-thr_avg-signal182.607666
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal748.728027
Spike_AFFX-r2-Bs-phe_5_signal93.312874
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1069.764160
RawQ2.174304
Spike_AFFX-r2-Bs-lys_5_signal44.472637
Signal(A)3.995446
%A34.322666
Signal(All)141.511826
Corner+Avg:77,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal256.458038
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal88.409119
Spike_AFFX-r2-Ec-bioD_avg-signal909.246094
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.686981
Spike_AFFX-r2-Bs-lys_avg-signal48.188679
Spike_AFFX-r2-P1-cre_avg-signal3472.376465
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.990355
Spike_AFFX-r2-Bs-thr_3_signal309.941772
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-signal88.291084
Spike_AFFX-r2-Bs-dap_3_signal499.127502
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.428775
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal239.664764
#M454
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal61.409916
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.070070
Spike_AFFX-r2-Bs-thr_M_signal173.352631
Signal(P)219.580673
Spike_AFFX-r2-Bs-phe_3-5-ratio0.947448
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4867,Count:9
Spike_AFFX-r2-P1-cre_5_signal3243.384766
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7829
Signal(M)14.880843
BackgroundAvg:53.11,Std:0.30,Min:52.3,Max:54.2
Spike_AFFX-r2-Ec-bioC_avg-signal248.061401
Spike_AFFX-r2-Bs-dap_avg-signal346.581055
Spike_AFFX-r2-Bs-dap_3-5-ratio3.250118
Spike_AFFX-r2-Ec-bioB_5_signal65.998215
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.521169
NF1.000000
HZ4
Tau0.015000

Slide: Astley_534-5_PPDK-mutant_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 ("Astley_534-5_PPDK-mutant_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: Astley_534-5_PPDK-mutant_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_116158 (AO) (BT)
Stock Code: N616158
Genetic Background: Col-0 (Columbia, N60000)
Age: 2 days old
Growth Conditions:
StratificationAfter sowing, seed was incubated at 4 oC in the dark for 3 days.
SterilisationSeed was rinsed briefly in 70 % (v/v) ethanol (Fisher Scientific) before being soaked in 10 % (v/v) sodium hypochlorite (Fisher Scientific) for 20 min. Seed was then rinsed three times in sterile water.
ProtocolSterilised seed was sown under sterile conditions onto 20 um nylon mesh (Normesh Limited) over 10 ml medium in 60 ml containers (Sterilin) with loosely fitted lids sealed with Micropore surgical tape (3M). Seed was stratified for 3 days before being subjected to a 30 min light pulse at 200 umol m-2 s-1 photosynthetically active radiation and 24 oC. Seed was then maintined in the dark at 24 oC for 2 days before tissue was harvested.
Percentage Agrose0.8
Substrate Sterilising ProcedureMedia was sterilised by autoclaving for 1.5 h.
Plant SpacingApprox. 100 per square cm
Temperature24 °C average, 24 °C day, 24 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by GE Healthcare. Intensity: 200µEinsteins. Wavelength: White)10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Genetic Variation: T-DNA Insertion
Tissue: whole plant
Additional Organism Information:
Sample Description2 day old whole etiolated seedlings
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:0.415792
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-ratio1.092199
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.971658
Spike_AFFX-r2-Bs-dap_5_signal148.949982
NoiseAvg:2.83,Std:0.07,Min:2.7,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal55.010963
#P14992
Spike_AFFX-r2-Bs-phe_M_signal68.896584
Corner-Avg:9102,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal79.326920
Spike_AFFX-r2-Ec-bioB_3_signal55.672188
Spike_AFFX-r2-Bs-lys_M_signal32.194683
Spike_AFFX-r2-P1-cre_3_signal3324.110107
Spike_AFFX-r2-Bs-lys_3-5-ratio1.284325
Spike_AFFX-r2-Bs-dap_M_signal328.709259
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.429837
Spike_AFFX-r2-Ec-bioB_avg-signal64.098404
Spike_AFFX-r2-Bs-thr_avg-signal150.547821
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal727.220703
Spike_AFFX-r2-Bs-phe_5_signal90.402878
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1038.928589
RawQ2.519328
Spike_AFFX-r2-Bs-lys_5_signal43.824982
Signal(A)3.475607
%A32.674267
Signal(All)137.750092
Corner+Avg:121,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal256.485809
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal88.282181
Spike_AFFX-r2-Ec-bioD_avg-signal883.074646
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.725555
Spike_AFFX-r2-Bs-lys_avg-signal44.101727
Spike_AFFX-r2-P1-cre_avg-signal3183.805664
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.600175
Spike_AFFX-r2-Bs-thr_3_signal243.689590
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-signal82.527214
Spike_AFFX-r2-Bs-dap_3_signal558.495789
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.428629
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal221.229538
#M365
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal56.285507
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.159365
Spike_AFFX-r2-Bs-thr_M_signal152.942902
Signal(P)207.531754
Spike_AFFX-r2-Bs-phe_3-5-ratio0.976542
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6938,Count:9
Spike_AFFX-r2-P1-cre_5_signal3043.500977
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7453
Signal(M)13.314857
BackgroundAvg:64.67,Std:0.72,Min:62.4,Max:66.3
Spike_AFFX-r2-Ec-bioC_avg-signal238.857666
Spike_AFFX-r2-Bs-dap_avg-signal345.385010
Spike_AFFX-r2-Bs-dap_3-5-ratio3.749552
Spike_AFFX-r2-Ec-bioB_5_signal57.296097
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.415792
NF1.000000
HZ4
Tau0.015000

Slide: Astley_534-6_PPDK-mutant_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 ("Astley_534-6_PPDK-mutant_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: Astley_534-6_PPDK-mutant_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_116158 (AO) (BT)
Stock Code: N616158
Genetic Background: Col-0 (Columbia, N60000)
Age: 2 days old
Growth Conditions:
StratificationAfter sowing, seed was incubated at 4 oC in the dark for 3 days.
SterilisationSeed was rinsed briefly in 70 % (v/v) ethanol (Fisher Scientific) before being soaked in 10 % (v/v) sodium hypochlorite (Fisher Scientific) for 20 min. Seed was then rinsed three times in sterile water.
ProtocolSterilised seed was sown under sterile conditions onto 20 um nylon mesh (Normesh Limited) over 10 ml medium in 60 ml containers (Sterilin) with loosely fitted lids sealed with Micropore surgical tape (3M). Seed was stratified for 3 days before being subjected to a 30 min light pulse at 200 umol m-2 s-1 photosynthetically active radiation and 24 oC. Seed was then maintined in the dark at 24 oC for 2 days before tissue was harvested.
Percentage Agrose0.8
Substrate Sterilising ProcedureMedia was sterilised by autoclaving for 1.5 h.
Plant SpacingApprox. 100 per square cm
Temperature24 °C average, 24 °C day, 24 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by GE Healthcare. Intensity: 200µEinsteins. Wavelength: White)10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Genetic Variation: T-DNA Insertion
Tissue: whole plant
Additional Organism Information:
Sample Description2 day old whole etiolated seedlings
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:0.586799
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-ratio1.052249
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.278119
Spike_AFFX-r2-Bs-dap_5_signal134.772980
NoiseAvg:2.95,Std:0.08,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_signal74.791946
#P14357
Spike_AFFX-r2-Bs-phe_M_signal75.781586
Corner-Avg:5878,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal49.324413
Spike_AFFX-r2-Ec-bioB_3_signal38.216923
Spike_AFFX-r2-Bs-lys_M_signal40.665386
Spike_AFFX-r2-P1-cre_3_signal2334.370605
Spike_AFFX-r2-Bs-lys_3-5-ratio1.480127
Spike_AFFX-r2-Bs-dap_M_signal344.664642
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.610099
Spike_AFFX-r2-Ec-bioB_avg-signal39.147415
Spike_AFFX-r2-Bs-thr_avg-signal230.713684
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal410.783569
Spike_AFFX-r2-Bs-phe_5_signal117.133560
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal654.999329
RawQ2.674171
Spike_AFFX-r2-Bs-lys_5_signal59.588150
Signal(A)4.838071
%A35.287155
Signal(All)136.837143
Corner+Avg:79,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal141.387268
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal105.705833
Spike_AFFX-r2-Ec-bioD_avg-signal532.891479
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.941692
Spike_AFFX-r2-Bs-lys_avg-signal62.817181
Spike_AFFX-r2-P1-cre_avg-signal2276.414795
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.771153
Spike_AFFX-r2-Bs-thr_3_signal419.590210
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal99.540321
Spike_AFFX-r2-Bs-dap_3_signal573.453308
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.594512
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal128.242905
#M404
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal88.198006
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.102496
Spike_AFFX-r2-Bs-thr_M_signal197.758896
Signal(P)214.210983
Spike_AFFX-r2-Bs-phe_3-5-ratio0.902439
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:3789,Count:9
Spike_AFFX-r2-P1-cre_5_signal2218.458984
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8049
Signal(M)17.045877
BackgroundAvg:73.16,Std:0.57,Min:71.5,Max:74.6
Spike_AFFX-r2-Ec-bioC_avg-signal134.815094
Spike_AFFX-r2-Bs-dap_avg-signal350.963623
Spike_AFFX-r2-Bs-dap_3-5-ratio4.254958
Spike_AFFX-r2-Ec-bioB_5_signal29.900913
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.586799
NF1.000000
HZ4
Tau0.015000

Slide: Astley_534-7_PCK-mutant_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 ("Astley_534-7_PCK-mutant_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: Astley_534-7_PCK-mutant_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_032133 (D) (AE)
Stock Code: N532133
Genetic Background: Col-0 (Columbia, N60000)
Age: 2 days old
Growth Conditions:
StratificationAfter sowing, seed was incubated at 4 oC in the dark for 3 days.
SterilisationSeed was rinsed briefly in 70 % (v/v) ethanol (Fisher Scientific) before being soaked in 10 % (v/v) sodium hypochlorite (Fisher Scientific) for 20 min. Seed was then rinsed three times in sterile water.
ProtocolSterilised seed was sown under sterile conditions onto 20 um nylon mesh (Normesh Limited) over 10 ml medium in 60 ml containers (Sterilin) with loosely fitted lids sealed with Micropore surgical tape (3M). Seed was stratified for 3 days before being subjected to a 30 min light pulse at 200 umol m-2 s-1 photosynthetically active radiation and 24 oC. Seed was then maintined in the dark at 24 oC for 2 days before tissue was harvested.
Percentage Agrose0.8
Substrate Sterilising ProcedureMedia was sterilised by autoclaving for 1.5 h.
Plant SpacingApprox. 100 per square cm
Temperature24 °C average, 24 °C day, 24 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by GE Healthcare. Intensity: 200µEinsteins. Wavelength: White)10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Genetic Variation: T-DNA Insertion
Tissue: whole plant
Additional Organism Information:
Sample Description2 day old whole etiolated seedlings
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:0.51278
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-ratio1.059534
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.967251
Spike_AFFX-r2-Bs-dap_5_signal173.622452
NoiseAvg:2.32,Std:0.08,Min:2.1,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal81.145897
#P14439
Spike_AFFX-r2-Bs-phe_M_signal103.560806
Corner-Avg:7554,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal91.654747
Spike_AFFX-r2-Ec-bioB_3_signal62.078575
Spike_AFFX-r2-Bs-lys_M_signal46.559822
Spike_AFFX-r2-P1-cre_3_signal3518.580322
Spike_AFFX-r2-Bs-lys_3-5-ratio1.426069
Spike_AFFX-r2-Bs-dap_M_signal410.756409
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.947638
Spike_AFFX-r2-Ec-bioB_avg-signal72.637924
Spike_AFFX-r2-Bs-thr_avg-signal226.797501
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal672.971375
Spike_AFFX-r2-Bs-phe_5_signal134.818237
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1055.894043
RawQ2.127119
Spike_AFFX-r2-Bs-lys_5_signal57.788177
Signal(A)3.543616
%A34.927662
Signal(All)141.697983
Corner+Avg:80,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal262.969116
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal118.140526
Spike_AFFX-r2-Ec-bioD_avg-signal864.432739
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.301182
Spike_AFFX-r2-Bs-lys_avg-signal62.252636
Spike_AFFX-r2-P1-cre_avg-signal3419.728516
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.771153
Spike_AFFX-r2-Bs-thr_3_signal401.480469
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-signal118.839851
Spike_AFFX-r2-Bs-dap_3_signal614.071655
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.569003
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal241.894745
#M404
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal82.409912
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.087122
Spike_AFFX-r2-Bs-thr_M_signal197.766190
Signal(P)221.515518
Spike_AFFX-r2-Bs-phe_3-5-ratio0.876295
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5149,Count:9
Spike_AFFX-r2-P1-cre_5_signal3320.876709
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7967
Signal(M)13.456743
BackgroundAvg:54.72,Std:0.51,Min:53.5,Max:56.0
Spike_AFFX-r2-Ec-bioC_avg-signal252.431931
Spike_AFFX-r2-Bs-dap_avg-signal399.483521
Spike_AFFX-r2-Bs-dap_3-5-ratio3.536822
Spike_AFFX-r2-Ec-bioB_5_signal64.180450
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.512780
NF1.000000
HZ4
Tau0.015000

Slide: Astley_534-8_PCK-mutant_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 ("Astley_534-8_PCK-mutant_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: Astley_534-8_PCK-mutant_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_032133 (D) (AE)
Stock Code: N532133
Genetic Background: Col-0 (Columbia, N60000)
Age: 2 days old
Growth Conditions:
StratificationAfter sowing, seed was incubated at 4 oC in the dark for 3 days.
SterilisationSeed was rinsed briefly in 70 % (v/v) ethanol (Fisher Scientific) before being soaked in 10 % (v/v) sodium hypochlorite (Fisher Scientific) for 20 min. Seed was then rinsed three times in sterile water.
ProtocolSterilised seed was sown under sterile conditions onto 20 um nylon mesh (Normesh Limited) over 10 ml medium in 60 ml containers (Sterilin) with loosely fitted lids sealed with Micropore surgical tape (3M). Seed was stratified for 3 days before being subjected to a 30 min light pulse at 200 umol m-2 s-1 photosynthetically active radiation and 24 oC. Seed was then maintined in the dark at 24 oC for 2 days before tissue was harvested.
Percentage Agrose0.8
Substrate Sterilising ProcedureMedia was sterilised by autoclaving for 1.5 h.
Plant SpacingApprox. 100 per square cm
Temperature24 °C average, 24 °C day, 24 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by GE Healthcare. Intensity: 200µEinsteins. Wavelength: White)10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Genetic Variation: T-DNA Insertion
Tissue: whole plant
Additional Organism Information:
Sample Description2 day old whole etiolated seedlings
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:0.51451
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-ratio1.055356
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.000780
Spike_AFFX-r2-Bs-dap_5_signal222.720901
NoiseAvg:2.61,Std:0.08,Min:2.4,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal81.455536
#P14642
Spike_AFFX-r2-Bs-phe_M_signal106.165001
Corner-Avg:8929,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal86.689110
Spike_AFFX-r2-Ec-bioB_3_signal51.918945
Spike_AFFX-r2-Bs-lys_M_signal52.846329
Spike_AFFX-r2-P1-cre_3_signal3764.203369
Spike_AFFX-r2-Bs-lys_3-5-ratio1.457594
Spike_AFFX-r2-Bs-dap_M_signal446.460297
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.553799
Spike_AFFX-r2-Ec-bioB_avg-signal63.495510
Spike_AFFX-r2-Bs-thr_avg-signal248.214600
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal724.502502
Spike_AFFX-r2-Bs-phe_5_signal144.179123
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1029.917480
RawQ2.372127
Spike_AFFX-r2-Bs-lys_5_signal68.892250
Signal(A)3.980876
%A33.853573
Signal(All)141.300369
Corner+Avg:100,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal246.609222
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal145.892868
Spike_AFFX-r2-Ec-bioD_avg-signal877.209961
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.191147
Spike_AFFX-r2-Bs-lys_avg-signal74.051826
Spike_AFFX-r2-P1-cre_avg-signal3665.481934
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_signal452.387665
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-signal132.078995
Spike_AFFX-r2-Bs-dap_3_signal726.142761
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.421551
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal216.868866
#M446
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal100.416908
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.137135
Spike_AFFX-r2-Bs-thr_M_signal210.800583
Signal(P)217.573898
Spike_AFFX-r2-Bs-phe_3-5-ratio1.011886
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7015,Count:9
Spike_AFFX-r2-P1-cre_5_signal3566.760742
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7722
Signal(M)14.807282
BackgroundAvg:59.24,Std:0.45,Min:58.1,Max:60.6
Spike_AFFX-r2-Ec-bioC_avg-signal231.739044
Spike_AFFX-r2-Bs-dap_avg-signal465.108002
Spike_AFFX-r2-Bs-dap_3-5-ratio3.260326
Spike_AFFX-r2-Ec-bioB_5_signal51.878464
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.514510
NF1.000000
HZ4
Tau0.015000

Slide: Astley_534-9_PCK-mutant_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 ("Astley_534-9_PCK-mutant_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: Astley_534-9_PCK-mutant_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_032133 (D) (AE)
Stock Code: N532133
Genetic Background: Col-0 (Columbia, N60000)
Age: 2 days old
Growth Conditions:
StratificationAfter sowing, seed was incubated at 4 oC in the dark for 3 days.
SterilisationSeed was rinsed briefly in 70 % (v/v) ethanol (Fisher Scientific) before being soaked in 10 % (v/v) sodium hypochlorite (Fisher Scientific) for 20 min. Seed was then rinsed three times in sterile water.
ProtocolSterilised seed was sown under sterile conditions onto 20 um nylon mesh (Normesh Limited) over 10 ml medium in 60 ml containers (Sterilin) with loosely fitted lids sealed with Micropore surgical tape (3M). Seed was stratified for 3 days before being subjected to a 30 min light pulse at 200 umol m-2 s-1 photosynthetically active radiation and 24 oC. Seed was then maintined in the dark at 24 oC for 2 days before tissue was harvested.
Percentage Agrose0.8
Substrate Sterilising ProcedureMedia was sterilised by autoclaving for 1.5 h.
Plant SpacingApprox. 100 per square cm
Temperature24 °C average, 24 °C day, 24 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by GE Healthcare. Intensity: 200µEinsteins. Wavelength: White)10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Genetic Variation: T-DNA Insertion
Tissue: whole plant
Additional Organism Information:
Sample Description2 day old whole etiolated seedlings
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:0.737784
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-ratio1.152262
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.894750
Spike_AFFX-r2-Bs-dap_5_signal282.781525
NoiseAvg:2.21,Std:0.05,Min:2.1,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_signal99.914978
#P14093
Spike_AFFX-r2-Bs-phe_M_signal130.655396
Corner-Avg:7104,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal113.301842
Spike_AFFX-r2-Ec-bioB_3_signal73.707520
Spike_AFFX-r2-Bs-lys_M_signal67.350616
Spike_AFFX-r2-P1-cre_3_signal4985.875488
Spike_AFFX-r2-Bs-lys_3-5-ratio1.142028
Spike_AFFX-r2-Bs-dap_M_signal602.705933
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.283258
Spike_AFFX-r2-Ec-bioB_avg-signal89.795715
Spike_AFFX-r2-Bs-thr_avg-signal304.276367
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal929.109497
Spike_AFFX-r2-Bs-phe_5_signal152.528427
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1236.845337
RawQ2.130430
Spike_AFFX-r2-Bs-lys_5_signal73.633209
Signal(A)4.621240
%A36.159580
Signal(All)146.462601
Corner+Avg:74,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal367.587250
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal159.567337
Spike_AFFX-r2-Ec-bioD_avg-signal1082.977417
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.784306
Spike_AFFX-r2-Bs-lys_avg-signal75.025002
Spike_AFFX-r2-P1-cre_avg-signal4656.454102
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.056116
Spike_AFFX-r2-Bs-thr_3_signal527.876587
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-signal147.583725
Spike_AFFX-r2-Bs-dap_3_signal734.541077
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.331216
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal339.807526
#M469
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal84.091179
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.081751
Spike_AFFX-r2-Bs-thr_M_signal285.037537
Signal(P)233.815262
Spike_AFFX-r2-Bs-phe_3-5-ratio1.046148
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5084,Count:9
Spike_AFFX-r2-P1-cre_5_signal4327.033203
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8248
Signal(M)16.070940
BackgroundAvg:56.97,Std:0.58,Min:55.5,Max:58.4
Spike_AFFX-r2-Ec-bioC_avg-signal353.697388
Spike_AFFX-r2-Bs-dap_avg-signal540.009521
Spike_AFFX-r2-Bs-dap_3-5-ratio2.597557
Spike_AFFX-r2-Ec-bioB_5_signal82.377777
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.737784
NF1.000000
HZ4
Tau0.015000

Slide: Astley_534-10_PPDK-PCK-mutant_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 ("Astley_534-10_PPDK-PCK-mutant_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: Astley_534-10_PPDK-PCK-mutant_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: PPDK PCK double insertional mutant
Stock Code:
Genetic Background: Col-0
Age: 2 days old
Growth Conditions:
StratificationAfter sowing, seed was incubated at 4 oC in the dark for 3 days.
SterilisationSeed was rinsed briefly in 70 % (v/v) ethanol (Fisher Scientific) before being soaked in 10 % (v/v) sodium hypochlorite (Fisher Scientific) for 20 min. Seed was then rinsed three times in sterile water.
ProtocolSterilised seed was sown under sterile conditions onto 20 um nylon mesh (Normesh Limited) over 10 ml medium in 60 ml containers (Sterilin) with loosely fitted lids sealed with Micropore surgical tape (3M). Seed was stratified for 3 days before being subjected to a 30 min light pulse at 200 umol m-2 s-1 photosynthetically active radiation and 24 oC. Seed was then maintined in the dark at 24 oC for 2 days before tissue was harvested.
Percentage Agrose0.8
Substrate Sterilising ProcedureMedia was sterilised by autoclaving for 1.5 h.
Plant SpacingApprox. 100 per square cm
Temperature24 °C average, 24 °C day, 24 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by GE Healthcare. Intensity: 200µEinsteins. Wavelength: White)10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Genetic Variation: T-DNA knock out mutation in At4g15530,At4g37870
Tissue: whole plant
Additional Organism Information:
Sample Description2 day old whole etiolated seedlings
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:0.901069
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-ratio0.937428
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.867844
Spike_AFFX-r2-Bs-dap_5_signal176.967041
NoiseAvg:2.15,Std:0.08,Min:1.9,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_signal72.195641
#P13541
Spike_AFFX-r2-Bs-phe_M_signal106.496925
Corner-Avg:7112,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal103.441483
Spike_AFFX-r2-Ec-bioB_3_signal65.363869
Spike_AFFX-r2-Bs-lys_M_signal52.144829
Spike_AFFX-r2-P1-cre_3_signal3858.479248
Spike_AFFX-r2-Bs-lys_3-5-ratio1.398757
Spike_AFFX-r2-Bs-dap_M_signal383.043091
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.517889
Spike_AFFX-r2-Ec-bioB_avg-signal81.374298
Spike_AFFX-r2-Bs-thr_avg-signal205.354050
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal780.123413
Spike_AFFX-r2-Bs-phe_5_signal90.862831
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1351.460938
RawQ2.004337
Spike_AFFX-r2-Bs-lys_5_signal54.800716
Signal(A)5.211613
%A38.553265
Signal(All)144.878296
Corner+Avg:77,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal336.527832
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal108.534462
Spike_AFFX-r2-Ec-bioD_avg-signal1065.792236
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.364315
Spike_AFFX-r2-Bs-lys_avg-signal61.199474
Spike_AFFX-r2-P1-cre_avg-signal3987.253906
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_signal326.171844
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal101.964745
Spike_AFFX-r2-Bs-dap_3_signal608.485046
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.732368
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal222.298447
#M475
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal76.652878
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.513856
Spike_AFFX-r2-Bs-thr_M_signal217.694656
Signal(P)239.990250
Spike_AFFX-r2-Bs-phe_3-5-ratio1.194487
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5177,Count:9
Spike_AFFX-r2-P1-cre_5_signal4116.028809
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8794
Signal(M)19.231922
BackgroundAvg:52.34,Std:0.35,Min:51.3,Max:53.4
Spike_AFFX-r2-Ec-bioC_avg-signal279.413147
Spike_AFFX-r2-Bs-dap_avg-signal389.498383
Spike_AFFX-r2-Bs-dap_3-5-ratio3.438409
Spike_AFFX-r2-Ec-bioB_5_signal75.317543
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.901069
NF1.000000
HZ4
Tau0.015000

Slide: Astley_534-11_PPDK-PCK-mutant_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 ("Astley_534-11_PPDK-PCK-mutant_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: Astley_534-11_PPDK-PCK-mutant_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: PPDK PCK double insertional mutant
Stock Code:
Genetic Background: Col-0
Age: 2 days old
Growth Conditions:
StratificationAfter sowing, seed was incubated at 4 oC in the dark for 3 days.
SterilisationSeed was rinsed briefly in 70 % (v/v) ethanol (Fisher Scientific) before being soaked in 10 % (v/v) sodium hypochlorite (Fisher Scientific) for 20 min. Seed was then rinsed three times in sterile water.
ProtocolSterilised seed was sown under sterile conditions onto 20 um nylon mesh (Normesh Limited) over 10 ml medium in 60 ml containers (Sterilin) with loosely fitted lids sealed with Micropore surgical tape (3M). Seed was stratified for 3 days before being subjected to a 30 min light pulse at 200 umol m-2 s-1 photosynthetically active radiation and 24 oC. Seed was then maintined in the dark at 24 oC for 2 days before tissue was harvested.
Percentage Agrose0.8
Substrate Sterilising ProcedureMedia was sterilised by autoclaving for 1.5 h.
Plant SpacingApprox. 100 per square cm
Temperature24 °C average, 24 °C day, 24 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by GE Healthcare. Intensity: 200µEinsteins. Wavelength: White)10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Genetic Variation: T-DNA knock out mutation in At4g15530,At4g37870
Tissue: whole plant
Additional Organism Information:
Sample Description2 day old whole etiolated seedlings
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:0.77107
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-ratio1.034346
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.959317
Spike_AFFX-r2-Bs-dap_5_signal408.171387
NoiseAvg:2.20,Std:0.11,Min:1.9,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal172.622406
#P13371
Spike_AFFX-r2-Bs-phe_M_signal197.267822
Corner-Avg:8993,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal174.875702
Spike_AFFX-r2-Ec-bioB_3_signal126.622429
Spike_AFFX-r2-Bs-lys_M_signal126.980797
Spike_AFFX-r2-P1-cre_3_signal6324.312988
Spike_AFFX-r2-Bs-lys_3-5-ratio1.424254
Spike_AFFX-r2-Bs-dap_M_signal887.615540
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.565232
Spike_AFFX-r2-Ec-bioB_avg-signal144.496811
Spike_AFFX-r2-Bs-thr_avg-signal460.960907
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1547.728882
Spike_AFFX-r2-Bs-phe_5_signal212.622070
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2129.379639
RawQ2.248477
Spike_AFFX-r2-Bs-lys_5_signal116.423042
Signal(A)4.580709
%A39.416924
Signal(All)152.205490
Corner+Avg:129,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal556.313416
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal205.882980
Spike_AFFX-r2-Ec-bioD_avg-signal1838.554199
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.619026
Spike_AFFX-r2-Bs-lys_avg-signal136.406601
Spike_AFFX-r2-P1-cre_avg-signal6219.310547
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.964051
Spike_AFFX-r2-Bs-thr_3_signal788.061340
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-signal205.257629
Spike_AFFX-r2-Bs-dap_3_signal1294.272095
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.375809
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal450.919495
#M448
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal165.815964
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.233731
Spike_AFFX-r2-Bs-thr_M_signal422.198944
Signal(P)255.976257
Spike_AFFX-r2-Bs-phe_3-5-ratio0.968305
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6876,Count:9
Spike_AFFX-r2-P1-cre_5_signal6114.308594
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8991
Signal(M)17.776087
BackgroundAvg:54.32,Std:0.37,Min:53.6,Max:55.8
Spike_AFFX-r2-Ec-bioC_avg-signal503.616455
Spike_AFFX-r2-Bs-dap_avg-signal863.353027
Spike_AFFX-r2-Bs-dap_3-5-ratio3.170903
Spike_AFFX-r2-Ec-bioB_5_signal131.992294
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.771070
NF1.000000
HZ4
Tau0.015000

Slide: Astley_534-12_PPDK-PCK-mutant_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 ("Astley_534-12_PPDK-PCK-mutant_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: Astley_534-12_PPDK-PCK-mutant_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: PPDK PCK double insertional mutant
Stock Code:
Genetic Background: Col-0
Age: 2 days old
Growth Conditions:
StratificationAfter sowing, seed was incubated at 4 oC in the dark for 3 days.
SterilisationSeed was rinsed briefly in 70 % (v/v) ethanol (Fisher Scientific) before being soaked in 10 % (v/v) sodium hypochlorite (Fisher Scientific) for 20 min. Seed was then rinsed three times in sterile water.
ProtocolSterilised seed was sown under sterile conditions onto 20 um nylon mesh (Normesh Limited) over 10 ml medium in 60 ml containers (Sterilin) with loosely fitted lids sealed with Micropore surgical tape (3M). Seed was stratified for 3 days before being subjected to a 30 min light pulse at 200 umol m-2 s-1 photosynthetically active radiation and 24 oC. Seed was then maintined in the dark at 24 oC for 2 days before tissue was harvested.
Percentage Agrose0.8
Substrate Sterilising ProcedureMedia was sterilised by autoclaving for 1.5 h.
Plant SpacingApprox. 100 per square cm
Temperature24 °C average, 24 °C day, 24 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by GE Healthcare. Intensity: 200µEinsteins. Wavelength: White)10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)0.7
Genetic Variation: T-DNA knock out mutation in At4g15530,At4g37870
Tissue: whole plant
Additional Organism Information:
Sample Description2 day old whole etiolated seedlings
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:0.681748
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-ratio1.064094
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.866669
Spike_AFFX-r2-Bs-dap_5_signal231.773651
NoiseAvg:2.25,Std:0.06,Min:2.1,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal111.210732
#P14005
Spike_AFFX-r2-Bs-phe_M_signal123.158257
Corner-Avg:6316,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal117.857178
Spike_AFFX-r2-Ec-bioB_3_signal72.202126
Spike_AFFX-r2-Bs-lys_M_signal60.714008
Spike_AFFX-r2-P1-cre_3_signal4105.766113
Spike_AFFX-r2-Bs-lys_3-5-ratio1.602934
Spike_AFFX-r2-Bs-dap_M_signal546.327759
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.779051
Spike_AFFX-r2-Ec-bioB_avg-signal91.123055
Spike_AFFX-r2-Bs-thr_avg-signal303.809906
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal736.757935
Spike_AFFX-r2-Bs-phe_5_signal196.099503
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1303.093262
RawQ2.170043
Spike_AFFX-r2-Bs-lys_5_signal70.624985
Signal(A)4.811076
%A36.527840
Signal(All)142.726501
Corner+Avg:76,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal270.738770
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal168.760498
Spike_AFFX-r2-Ec-bioD_avg-signal1019.925598
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.398510
Spike_AFFX-r2-Bs-lys_avg-signal81.515388
Spike_AFFX-r2-P1-cre_avg-signal3982.113281
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.073652
Spike_AFFX-r2-Bs-thr_3_signal531.481812
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-signal162.672745
Spike_AFFX-r2-Bs-dap_3_signal856.619934
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.768686
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal286.986572
#M473
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal113.207184
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.943385
Spike_AFFX-r2-Bs-thr_M_signal268.737122
Signal(P)228.999939
Spike_AFFX-r2-Bs-phe_3-5-ratio0.860586
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4515,Count:9
Spike_AFFX-r2-P1-cre_5_signal3858.460205
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8332
Signal(M)17.677114
BackgroundAvg:57.11,Std:0.64,Min:55.3,Max:58.8
Spike_AFFX-r2-Ec-bioC_avg-signal278.862671
Spike_AFFX-r2-Bs-dap_avg-signal544.907166
Spike_AFFX-r2-Bs-dap_3-5-ratio3.695933
Spike_AFFX-r2-Ec-bioB_5_signal83.309875
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.681748
NF1.000000
HZ4
Tau0.015000

Hybridisation Set: mouse: ummm, cheese


Problems? Comments? Suggestions? Contact the Affymetrix Team