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Experiment: Comparison of silenced type II NAD(P)H dehydrogenase genes

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-566

Type II NAD(P)H dehydrogenases bypass the energy-conserving steps in the plant mitochondrial electron transport chain. In this investigation we suppressed NDA1 and NDA2 with one RNAi construct, and separately, NDB1 with another construct. Both NDA1,2- and NDB1-suppressing plants displayed lowered level of transcript for the respective target genes. Also, the plants of both lines showed a small but significant decrease in biomass accumulation, as compared to the wild type. To investigate the putative transcriptomic effects of the gene silencing we grew plant in 10 h light period and harvested rosettes briefly before flowering for transcript analyses.

About the Experimenter

Name: Allan Rasmusson
Head of Lab Name: Allan Rasmusson
Lab:
Address:Department of Biology, Lund University
Biology Building, Solvegatan 35B, Lund, Skine lin, SE22362, SWEDEN
Postcode: SE22362
Country: SWEDEN
 

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
Number of Slides:15
 
Experimental Parameters:
parametergenetic_modification
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Rasmusson: Comparison of silenced type II NAD(P)H dehydrogenase genes

Slide: Rasmusson_566-1_WT_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 ("Rasmusson_566-1_WT_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: Rasmusson_566-1_WT_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia0
Stock Code:
Age: 35 days
Growth Conditions:
Stratification2 d, 4°C
ProtocolSeeds were sown, 3 per 10 cm pot, on a 1:1:2 ratio of perlite:vermiculite:soil, stratified 2 d at 4°C and then placed in 10 h of light, 80 µmol m-2 s-1, 24-25°C. Approximately two weeks after sowing, the plants were supplied with 0.5x Hoagland solution, with a resupply once a week. Watering was carried out by subirrigation in trays.
Temperature25 °C average, 25 °C day, 25 °C night
Humidity54 % average, 40 % day, 68 % night
Medium
Lighting(Source: High pressure sodium and metal halide manufactured by OSRAM, Germany. Intensity: 80µEinsteins. Wavelength: White)10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: Whole rosette
Additional Organism Information:
Sample DescriptionPlants were grown until shortly before the first flower bud became visible, and the whole rosettes were sampled.
Other Information:
ecotype_habitat

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:0.324466
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-ratio1.321908
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.446534
Spike_AFFX-r2-Bs-dap_5_signal49.134010
NoiseAvg:4.16,Std:0.12,Min:3.9,Max:4.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.458853
#P14378
Spike_AFFX-r2-Bs-phe_M_signal19.971153
Corner-Avg:13203,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal82.823479
Spike_AFFX-r2-Ec-bioB_3_signal76.358101
Spike_AFFX-r2-Bs-lys_M_signal4.933931
Spike_AFFX-r2-P1-cre_3_signal3706.116211
Spike_AFFX-r2-Bs-lys_3-5-ratio2.948821
Spike_AFFX-r2-Bs-dap_M_signal107.056320
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.632222
Spike_AFFX-r2-Ec-bioB_avg-signal70.656166
Spike_AFFX-r2-Bs-thr_avg-signal31.727587
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal689.845093
Spike_AFFX-r2-Bs-phe_5_signal15.025558
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1083.416870
RawQ3.346948
Spike_AFFX-r2-Bs-lys_5_signal9.946270
Signal(A)4.094345
%A35.116177
Signal(All)143.432251
Corner+Avg:226,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal263.213226
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal20.271456
Spike_AFFX-r2-Ec-bioD_avg-signal886.630981
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.033756
Spike_AFFX-r2-Bs-lys_avg-signal14.736656
Spike_AFFX-r2-P1-cre_avg-signal3254.863281
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.850066
Spike_AFFX-r2-Bs-thr_3_signal33.393391
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-signal18.422722
Spike_AFFX-r2-Bs-dap_3_signal142.884369
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.570522
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal223.435745
#M422
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal29.329769
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.178026
Spike_AFFX-r2-Bs-thr_M_signal41.330513
Signal(P)224.786316
Spike_AFFX-r2-Bs-phe_3-5-ratio1.349132
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9650,Count:9
Spike_AFFX-r2-P1-cre_5_signal2803.610596
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8010
Signal(M)16.389050
BackgroundAvg:79.91,Std:1.22,Min:77.2,Max:84.1
Spike_AFFX-r2-Ec-bioC_avg-signal243.324493
Spike_AFFX-r2-Bs-dap_avg-signal99.691566
Spike_AFFX-r2-Bs-dap_3-5-ratio2.908054
Spike_AFFX-r2-Ec-bioB_5_signal52.786934
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.324466
NF1.000000
HZ4
Tau0.015000

Slide: Rasmusson_566-2_WT_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 ("Rasmusson_566-2_WT_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: Rasmusson_566-2_WT_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia0
Stock Code:
Age: 35 days
Growth Conditions:
Stratification2 d, 4°C
ProtocolSeeds were sown, 3 per 10 cm pot, on a 1:1:2 ratio of perlite:vermiculite:soil, stratified 2 d at 4°C and then placed in 10 h of light, 80 µmol m-2 s-1, 24-25°C. Approximately two weeks after sowing, the plants were supplied with 0.5x Hoagland solution, with a resupply once a week. Watering was carried out by subirrigation in trays.
Temperature25 °C average, 25 °C day, 25 °C night
Humidity54 % average, 40 % day, 68 % night
Medium
Lighting(Source: High pressure sodium and metal halide manufactured by OSRAM, Germany. Intensity: 80µEinsteins. Wavelength: White)10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: Whole rosette
Additional Organism Information:
Sample DescriptionPlants were grown until shortly before the first flower bud became visible, and the whole rosettes were sampled.
Other Information:
ecotype_habitat

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:0.506863
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-ratio1.244394
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.324531
Spike_AFFX-r2-Bs-dap_5_signal50.306602
NoiseAvg:3.19,Std:0.12,Min:2.9,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal17.857870
#P13761
Spike_AFFX-r2-Bs-phe_M_signal28.056959
Corner-Avg:9364,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal83.668884
Spike_AFFX-r2-Ec-bioB_3_signal72.889481
Spike_AFFX-r2-Bs-lys_M_signal10.124312
Spike_AFFX-r2-P1-cre_3_signal4667.499023
Spike_AFFX-r2-Bs-lys_3-5-ratio2.239862
Spike_AFFX-r2-Bs-dap_M_signal130.842209
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.021476
Spike_AFFX-r2-Ec-bioB_avg-signal70.529594
Spike_AFFX-r2-Bs-thr_avg-signal50.853092
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal722.303406
Spike_AFFX-r2-Bs-phe_5_signal15.374941
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1275.476318
RawQ2.836133
Spike_AFFX-r2-Bs-lys_5_signal13.643991
Signal(A)5.174484
%A37.536167
Signal(All)151.645065
Corner+Avg:156,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal299.912445
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.423151
Spike_AFFX-r2-Ec-bioD_avg-signal998.889893
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.328804
Spike_AFFX-r2-Bs-lys_avg-signal18.109652
Spike_AFFX-r2-P1-cre_avg-signal4209.160156
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.135029
Spike_AFFX-r2-Bs-thr_3_signal89.672874
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-signal23.951683
Spike_AFFX-r2-Bs-dap_3_signal167.115646
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.765846
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal317.567627
#M487
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal30.560656
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.944405
Spike_AFFX-r2-Bs-thr_M_signal45.028549
Signal(P)247.450424
Spike_AFFX-r2-Bs-phe_3-5-ratio1.848667
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6221,Count:9
Spike_AFFX-r2-P1-cre_5_signal3750.821533
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8562
Signal(M)19.619814
BackgroundAvg:66.93,Std:0.33,Min:65.8,Max:67.9
Spike_AFFX-r2-Ec-bioC_avg-signal308.740051
Spike_AFFX-r2-Bs-dap_avg-signal116.088158
Spike_AFFX-r2-Bs-dap_3-5-ratio3.321943
Spike_AFFX-r2-Ec-bioB_5_signal55.030411
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.506863
NF1.000000
HZ4
Tau0.015000

Slide: Rasmusson_566-3_WT_Rep4_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 ("Rasmusson_566-3_WT_Rep4_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: Rasmusson_566-3_WT_Rep4_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia0
Stock Code:
Age: 35 days
Growth Conditions:
Stratification2 d, 4°C
ProtocolSeeds were sown, 3 per 10 cm pot, on a 1:1:2 ratio of perlite:vermiculite:soil, stratified 2 d at 4°C and then placed in 10 h of light, 80 µmol m-2 s-1, 24-25°C. Approximately two weeks after sowing, the plants were supplied with 0.5x Hoagland solution, with a resupply once a week. Watering was carried out by subirrigation in trays.
Temperature25 °C average, 25 °C day, 25 °C night
Humidity54 % average, 40 % day, 68 % night
Medium
Lighting(Source: High pressure sodium and metal halide manufactured by OSRAM, Germany. Intensity: 80µEinsteins. Wavelength: White)10 hour days, 14 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: Whole rosette
Additional Organism Information:
Sample DescriptionPlants were grown until shortly before the first flower bud became visible, and the whole rosettes were sampled.
Other Information:
ecotype_habitat

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:0.843631
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-ratio1.247516
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.099685
Spike_AFFX-r2-Bs-dap_5_signal83.412766
NoiseAvg:3.09,Std:0.26,Min:2.8,Max:4.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal44.889256
#P13414
Spike_AFFX-r2-Bs-phe_M_signal38.354584
Corner-Avg:9243,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal167.554626
Spike_AFFX-r2-Ec-bioB_3_signal129.718018
Spike_AFFX-r2-Bs-lys_M_signal17.488400
Spike_AFFX-r2-P1-cre_3_signal7241.492676
Spike_AFFX-r2-Bs-lys_3-5-ratio1.568497
Spike_AFFX-r2-Bs-dap_M_signal187.519638
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.378726
Spike_AFFX-r2-Ec-bioB_avg-signal138.410645
Spike_AFFX-r2-Bs-thr_avg-signal77.657257
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1095.609009
Spike_AFFX-r2-Bs-phe_5_signal36.994427
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2268.813965
RawQ2.916496
Spike_AFFX-r2-Bs-lys_5_signal18.142698
Signal(A)6.050593
%A39.145111
Signal(All)157.802322
Corner+Avg:141,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal490.841644
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal34.924847
Spike_AFFX-r2-Ec-bioD_avg-signal1682.211426
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.807541
Spike_AFFX-r2-Bs-lys_avg-signal21.362623
Spike_AFFX-r2-P1-cre_avg-signal6523.110840
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.047348
Spike_AFFX-r2-Bs-thr_3_signal106.779221
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal36.757954
Spike_AFFX-r2-Bs-dap_3_signal251.649948
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.070824
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal584.120056
#M467
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.456766
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.840310
Spike_AFFX-r2-Bs-thr_M_signal81.303291
Signal(P)263.546326
Spike_AFFX-r2-Bs-phe_3-5-ratio0.944057
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7271,Count:9
Spike_AFFX-r2-P1-cre_5_signal5804.729004
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8929
Signal(M)21.915575
BackgroundAvg:69.87,Std:0.39,Min:68.9,Max:70.9
Spike_AFFX-r2-Ec-bioC_avg-signal537.480835
Spike_AFFX-r2-Bs-dap_avg-signal174.194107
Spike_AFFX-r2-Bs-dap_3-5-ratio3.016924
Spike_AFFX-r2-Ec-bioB_5_signal117.959297
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.843631
NF1.000000
HZ4
Tau0.015000

Slide: Rasmusson_566-4_nda-17.11_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 ("Rasmusson_566-4_nda-17.11_Rep1_ATH1") was made from "" 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: Rasmusson_566-4_nda-17.11_Rep1_ATH1
Organism:
Stock Code:
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:0.985149
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-ratio1.200746
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.925631
Spike_AFFX-r2-Bs-dap_5_signal59.411045
NoiseAvg:3.35,Std:0.08,Min:3.1,Max:3.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal53.500835
#P12501
Spike_AFFX-r2-Bs-phe_M_signal16.298019
Corner-Avg:8835,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal129.299530
Spike_AFFX-r2-Ec-bioB_3_signal116.476112
Spike_AFFX-r2-Bs-lys_M_signal10.763552
Spike_AFFX-r2-P1-cre_3_signal7357.660645
Spike_AFFX-r2-Bs-lys_3-5-ratio2.540350
Spike_AFFX-r2-Bs-dap_M_signal118.656357
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.109178
Spike_AFFX-r2-Ec-bioB_avg-signal123.869965
Spike_AFFX-r2-Bs-thr_avg-signal82.946815
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1411.521362
Spike_AFFX-r2-Bs-phe_5_signal23.029425
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2177.043457
RawQ3.184298
Spike_AFFX-r2-Bs-lys_5_signal10.828051
Signal(A)8.696552
%A43.024990
Signal(All)160.569901
Corner+Avg:141,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal509.245178
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal30.270157
Spike_AFFX-r2-Ec-bioD_avg-signal1794.282471
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P54.804909
Spike_AFFX-r2-Bs-lys_avg-signal16.366213
Spike_AFFX-r2-P1-cre_avg-signal6742.617188
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.170101
Spike_AFFX-r2-Bs-thr_3_signal112.842773
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-signal23.199202
Spike_AFFX-r2-Bs-dap_3_signal198.930130
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.542338
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal549.897644
#M495
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.507036
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.926073
Spike_AFFX-r2-Bs-thr_M_signal82.496834
Signal(P)284.975708
Spike_AFFX-r2-Bs-phe_3-5-ratio1.314412
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6162,Count:9
Spike_AFFX-r2-P1-cre_5_signal6127.573242
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9814
Signal(M)29.838795
BackgroundAvg:76.65,Std:0.52,Min:75.3,Max:78.4
Spike_AFFX-r2-Ec-bioC_avg-signal529.571411
Spike_AFFX-r2-Bs-dap_avg-signal125.665840
Spike_AFFX-r2-Bs-dap_3-5-ratio3.348369
Spike_AFFX-r2-Ec-bioB_5_signal125.834259
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.985149
NF1.000000
HZ4
Tau0.015000

Slide: Rasmusson_566-5_nda-17.11_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 ("Rasmusson_566-5_nda-17.11_Rep2_ATH1") was made from "" 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: Rasmusson_566-5_nda-17.11_Rep2_ATH1
Organism:
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.119034
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-ratio1.173777
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.804884
Spike_AFFX-r2-Bs-dap_5_signal50.832909
NoiseAvg:3.10,Std:0.09,Min:2.9,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal32.247952
#P12250
Spike_AFFX-r2-Bs-phe_M_signal15.755319
Corner-Avg:8780,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal147.448059
Spike_AFFX-r2-Ec-bioB_3_signal122.810059
Spike_AFFX-r2-Bs-lys_M_signal9.830649
Spike_AFFX-r2-P1-cre_3_signal8094.007324
Spike_AFFX-r2-Bs-lys_3-5-ratio1.140400
Spike_AFFX-r2-Bs-dap_M_signal82.800598
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.874388
Spike_AFFX-r2-Ec-bioB_avg-signal140.946365
Spike_AFFX-r2-Bs-thr_avg-signal69.782219
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1512.837891
Spike_AFFX-r2-Bs-phe_5_signal20.121382
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2335.760254
RawQ3.017004
Spike_AFFX-r2-Bs-lys_5_signal28.375042
Signal(A)9.182033
%A43.954407
Signal(All)163.347092
Corner+Avg:135,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal582.218262
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal19.079496
Spike_AFFX-r2-Ec-bioD_avg-signal1924.299072
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P53.704517
Spike_AFFX-r2-Bs-lys_avg-signal23.521524
Spike_AFFX-r2-P1-cre_avg-signal7494.851074
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.341079
Spike_AFFX-r2-Bs-thr_3_signal92.693130
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.318733
Spike_AFFX-r2-Bs-dap_3_signal145.902817
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.543959
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal609.919067
#M534
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal32.358887
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.954583
Spike_AFFX-r2-Bs-thr_M_signal84.405571
Signal(P)295.256561
Spike_AFFX-r2-Bs-phe_3-5-ratio0.948220
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5595,Count:9
Spike_AFFX-r2-P1-cre_5_signal6895.694824
Spike_AFFX-r2-Bs-phe_M_detectionA
#A10026
Signal(M)31.826447
BackgroundAvg:72.33,Std:0.65,Min:70.9,Max:73.7
Spike_AFFX-r2-Ec-bioC_avg-signal596.068665
Spike_AFFX-r2-Bs-dap_avg-signal93.178772
Spike_AFFX-r2-Bs-dap_3-5-ratio2.870243
Spike_AFFX-r2-Ec-bioB_5_signal152.580978
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.119034
NF1.000000
HZ4
Tau0.015000

Slide: Rasmusson_566-6_nda-17.11_Rep4_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 ("Rasmusson_566-6_nda-17.11_Rep4_ATH1") was made from "" 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: Rasmusson_566-6_nda-17.11_Rep4_ATH1
Organism:
Stock Code:
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:0.621168
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-ratio1.164613
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.197051
Spike_AFFX-r2-Bs-dap_5_signal62.503796
NoiseAvg:3.52,Std:0.08,Min:3.3,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal40.153534
#P13508
Spike_AFFX-r2-Bs-phe_M_signal27.391788
Corner-Avg:12209,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal149.547287
Spike_AFFX-r2-Ec-bioB_3_signal128.791672
Spike_AFFX-r2-Bs-lys_M_signal11.444304
Spike_AFFX-r2-P1-cre_3_signal6205.137695
Spike_AFFX-r2-Bs-lys_3-5-ratio4.259255
Spike_AFFX-r2-Bs-dap_M_signal142.992233
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.806768
Spike_AFFX-r2-Ec-bioB_avg-signal128.643265
Spike_AFFX-r2-Bs-thr_avg-signal60.097198
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1203.054565
Spike_AFFX-r2-Bs-phe_5_signal12.872916
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2104.859863
RawQ3.221002
Spike_AFFX-r2-Bs-lys_5_signal9.453699
Signal(A)5.867620
%A38.768085
Signal(All)157.823944
Corner+Avg:190,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal461.769470
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.314980
Spike_AFFX-r2-Ec-bioD_avg-signal1653.957275
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.219639
Spike_AFFX-r2-Bs-lys_avg-signal20.387907
Spike_AFFX-r2-P1-cre_avg-signal5766.603516
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.012275
Spike_AFFX-r2-Bs-thr_3_signal72.548119
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal22.859894
Spike_AFFX-r2-Bs-dap_3_signal209.387299
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.749596
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal458.279419
#M459
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal40.265717
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.007616
Spike_AFFX-r2-Bs-thr_M_signal67.589951
Signal(P)261.951172
Spike_AFFX-r2-Bs-phe_3-5-ratio2.199578
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7610,Count:9
Spike_AFFX-r2-P1-cre_5_signal5328.069336
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8843
Signal(M)21.003441
BackgroundAvg:77.96,Std:0.85,Min:75.9,Max:79.3
Spike_AFFX-r2-Ec-bioC_avg-signal460.024445
Spike_AFFX-r2-Bs-dap_avg-signal138.294434
Spike_AFFX-r2-Bs-dap_3-5-ratio3.349993
Spike_AFFX-r2-Ec-bioB_5_signal107.590820
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.621168
NF1.000000
HZ4
Tau0.015000

Slide: Rasmusson_566-7_nda-26.6_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 ("Rasmusson_566-7_nda-26.6_Rep1_ATH1") was made from "" 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: Rasmusson_566-7_nda-26.6_Rep1_ATH1
Organism:
Stock Code:
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:0.814837
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-ratio1.140647
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.870733
Spike_AFFX-r2-Bs-dap_5_signal35.901218
NoiseAvg:4.01,Std:0.13,Min:3.7,Max:4.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal23.534348
#P12537
Spike_AFFX-r2-Bs-phe_M_signal19.703632
Corner-Avg:9360,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal94.610611
Spike_AFFX-r2-Ec-bioB_3_signal91.690483
Spike_AFFX-r2-Bs-lys_M_signal13.070573
Spike_AFFX-r2-P1-cre_3_signal6311.893066
Spike_AFFX-r2-Bs-lys_3-5-ratio1.585679
Spike_AFFX-r2-Bs-dap_M_signal76.788353
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.902212
Spike_AFFX-r2-Ec-bioB_avg-signal97.201233
Spike_AFFX-r2-Bs-thr_avg-signal36.670372
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1020.176208
Spike_AFFX-r2-Bs-phe_5_signal13.589109
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1981.381592
RawQ3.488587
Spike_AFFX-r2-Bs-lys_5_signal10.015698
Signal(A)8.910733
%A42.639194
Signal(All)160.174774
Corner+Avg:156,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal451.597595
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal19.512955
Spike_AFFX-r2-Ec-bioD_avg-signal1500.778931
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P54.962734
Spike_AFFX-r2-Bs-lys_avg-signal12.989319
Spike_AFFX-r2-P1-cre_avg-signal5922.750000
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.398071
Spike_AFFX-r2-Bs-thr_3_signal44.767319
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal17.601898
Spike_AFFX-r2-Bs-dap_3_signal92.652481
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.942195
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal464.449036
#M547
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal15.881686
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.972330
Spike_AFFX-r2-Bs-thr_M_signal41.709450
Signal(P)283.214355
Spike_AFFX-r2-Bs-phe_3-5-ratio1.435926
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7580,Count:9
Spike_AFFX-r2-P1-cre_5_signal5533.606445
Spike_AFFX-r2-Bs-phe_M_detectionA
#A9726
Signal(M)29.730188
BackgroundAvg:89.45,Std:0.71,Min:88.1,Max:91.0
Spike_AFFX-r2-Ec-bioC_avg-signal458.023315
Spike_AFFX-r2-Bs-dap_avg-signal68.447350
Spike_AFFX-r2-Bs-dap_3-5-ratio2.580761
Spike_AFFX-r2-Ec-bioB_5_signal105.302597
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.814837
NF1.000000
HZ4
Tau0.015000

Slide: Rasmusson_566-8_nda-26.6_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 ("Rasmusson_566-8_nda-26.6_Rep2_ATH1") was made from "" 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: Rasmusson_566-8_nda-26.6_Rep2_ATH1
Organism:
Stock Code:
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:0.480892
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-ratio1.259304
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.361740
Spike_AFFX-r2-Bs-dap_5_signal62.409916
NoiseAvg:3.74,Std:0.12,Min:3.5,Max:4.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal30.195576
#P13822
Spike_AFFX-r2-Bs-phe_M_signal22.132202
Corner-Avg:13336,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal135.378662
Spike_AFFX-r2-Ec-bioB_3_signal142.523514
Spike_AFFX-r2-Bs-lys_M_signal11.302602
Spike_AFFX-r2-P1-cre_3_signal6188.705566
Spike_AFFX-r2-Bs-lys_3-5-ratio1.699715
Spike_AFFX-r2-Bs-dap_M_signal129.535568
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.723425
Spike_AFFX-r2-Ec-bioB_avg-signal127.521645
Spike_AFFX-r2-Bs-thr_avg-signal45.891922
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1379.706421
Spike_AFFX-r2-Bs-phe_5_signal17.148893
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2133.424805
RawQ3.175380
Spike_AFFX-r2-Bs-lys_5_signal10.757929
Signal(A)4.729047
%A37.448486
Signal(All)154.342407
Corner+Avg:215,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal514.163635
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal27.249956
Spike_AFFX-r2-Ec-bioD_avg-signal1756.565674
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.596230
Spike_AFFX-r2-Bs-lys_avg-signal13.448647
Spike_AFFX-r2-P1-cre_avg-signal5551.545898
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_signal52.039822
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal22.177017
Spike_AFFX-r2-Bs-dap_3_signal174.305466
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.546289
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal500.105804
#M446
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.285410
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.028110
Spike_AFFX-r2-Bs-thr_M_signal55.440372
Signal(P)251.195724
Spike_AFFX-r2-Bs-phe_3-5-ratio1.589021
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9738,Count:9
Spike_AFFX-r2-P1-cre_5_signal4914.386719
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8542
Signal(M)18.223494
BackgroundAvg:80.86,Std:0.61,Min:79.6,Max:82.0
Spike_AFFX-r2-Ec-bioC_avg-signal507.134705
Spike_AFFX-r2-Bs-dap_avg-signal122.083649
Spike_AFFX-r2-Bs-dap_3-5-ratio2.792913
Spike_AFFX-r2-Ec-bioB_5_signal104.662796
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.480892
NF1.000000
HZ4
Tau0.015000

Slide: Rasmusson_566-9_nda-26.6_Rep4_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 ("Rasmusson_566-9_nda-26.6_Rep4_ATH1") was made from "" 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: Rasmusson_566-9_nda-26.6_Rep4_ATH1
Organism:
Stock Code:
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:0.916537
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-ratio1.154589
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.983883
Spike_AFFX-r2-Bs-dap_5_signal49.977467
NoiseAvg:2.60,Std:0.06,Min:2.4,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal34.859203
#P13660
Spike_AFFX-r2-Bs-phe_M_signal24.074358
Corner-Avg:5515,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal116.225777
Spike_AFFX-r2-Ec-bioB_3_signal92.128517
Spike_AFFX-r2-Bs-lys_M_signal9.235868
Spike_AFFX-r2-P1-cre_3_signal5079.513672
Spike_AFFX-r2-Bs-lys_3-5-ratio1.869355
Spike_AFFX-r2-Bs-dap_M_signal113.935349
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.739401
Spike_AFFX-r2-Ec-bioB_avg-signal100.663994
Spike_AFFX-r2-Bs-thr_avg-signal50.637054
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal744.584167
Spike_AFFX-r2-Bs-phe_5_signal19.929277
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1525.900879
RawQ2.509320
Spike_AFFX-r2-Bs-lys_5_signal12.470152
Signal(A)5.485451
%A38.149933
Signal(All)156.473480
Corner+Avg:83,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal365.860138
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal23.713539
Spike_AFFX-r2-Ec-bioD_avg-signal1135.242554
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.886013
Spike_AFFX-r2-Bs-lys_avg-signal15.005722
Spike_AFFX-r2-P1-cre_avg-signal4739.463379
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.964051
Spike_AFFX-r2-Bs-thr_3_signal60.634140
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionM
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal22.572390
Spike_AFFX-r2-Bs-dap_3_signal136.008484
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.049333
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal368.417114
#M448
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.311146
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.993060
Spike_AFFX-r2-Bs-thr_M_signal56.417812
Signal(P)257.148285
Spike_AFFX-r2-Bs-phe_3-5-ratio1.189885
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5290,Count:9
Spike_AFFX-r2-P1-cre_5_signal4399.413086
Spike_AFFX-r2-Bs-phe_M_detectionM
#A8702
Signal(M)19.598310
BackgroundAvg:58.25,Std:0.55,Min:56.8,Max:59.6
Spike_AFFX-r2-Ec-bioC_avg-signal367.138611
Spike_AFFX-r2-Bs-dap_avg-signal99.973763
Spike_AFFX-r2-Bs-dap_3-5-ratio2.721396
Spike_AFFX-r2-Ec-bioB_5_signal93.637680
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.916537
NF1.000000
HZ4
Tau0.015000

Slide: Rasmusson_566-10_ndb1-8.7_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 ("Rasmusson_566-10_ndb1-8.7_Rep1_ATH1") was made from "" 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: Rasmusson_566-10_ndb1-8.7_Rep1_ATH1
Organism:
Stock Code:
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:0.786041
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-ratio1.045319
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.340372
Spike_AFFX-r2-Bs-dap_5_signal44.305046
NoiseAvg:3.31,Std:0.08,Min:3.1,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal21.627058
#P13136
Spike_AFFX-r2-Bs-phe_M_signal9.380781
Corner-Avg:8478,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal126.779366
Spike_AFFX-r2-Ec-bioB_3_signal94.730118
Spike_AFFX-r2-Bs-lys_M_signal9.269081
Spike_AFFX-r2-P1-cre_3_signal5762.636719
Spike_AFFX-r2-Bs-lys_3-5-ratio2.260860
Spike_AFFX-r2-Bs-dap_M_signal78.622688
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.557552
Spike_AFFX-r2-Ec-bioB_avg-signal97.394676
Spike_AFFX-r2-Bs-thr_avg-signal39.007221
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1044.322388
Spike_AFFX-r2-Bs-phe_5_signal15.131103
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1748.136719
RawQ2.992003
Spike_AFFX-r2-Bs-lys_5_signal9.436138
Signal(A)7.196079
%A40.407715
Signal(All)156.360107
Corner+Avg:136,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal389.824677
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal14.160477
Spike_AFFX-r2-Ec-bioD_avg-signal1396.229492
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P57.588776
Spike_AFFX-r2-Bs-lys_avg-signal13.346336
Spike_AFFX-r2-P1-cre_avg-signal5637.719727
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.003507
Spike_AFFX-r2-Bs-thr_3_signal55.312321
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal12.890786
Spike_AFFX-r2-Bs-dap_3_signal98.461952
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.673944
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal436.767639
#M457
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.333790
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.892522
Spike_AFFX-r2-Bs-thr_M_signal40.082279
Signal(P)265.579010
Spike_AFFX-r2-Bs-phe_3-5-ratio0.935852
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6164,Count:9
Spike_AFFX-r2-P1-cre_5_signal5512.803223
Spike_AFFX-r2-Bs-phe_M_detectionA
#A9217
Signal(M)25.387033
BackgroundAvg:73.47,Std:1.09,Min:71.1,Max:76.9
Spike_AFFX-r2-Ec-bioC_avg-signal413.296143
Spike_AFFX-r2-Bs-dap_avg-signal73.796562
Spike_AFFX-r2-Bs-dap_3-5-ratio2.222364
Spike_AFFX-r2-Ec-bioB_5_signal70.674515
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.786041
NF1.000000
HZ4
Tau0.015000

Slide: Rasmusson_566-11_ndb1-8.7_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 ("Rasmusson_566-11_ndb1-8.7_Rep2_ATH1") was made from "" 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: Rasmusson_566-11_ndb1-8.7_Rep2_ATH1
Organism:
Stock Code:
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:0.665849
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-ratio1.288922
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.960226
Spike_AFFX-r2-Bs-dap_5_signal56.545231
NoiseAvg:3.22,Std:0.09,Min:3.0,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal23.439127
#P13493
Spike_AFFX-r2-Bs-phe_M_signal22.308075
Corner-Avg:9101,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal134.900894
Spike_AFFX-r2-Ec-bioB_3_signal107.815971
Spike_AFFX-r2-Bs-lys_M_signal7.180159
Spike_AFFX-r2-P1-cre_3_signal6574.542969
Spike_AFFX-r2-Bs-lys_3-5-ratio2.333475
Spike_AFFX-r2-Bs-dap_M_signal93.349663
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.599149
Spike_AFFX-r2-Ec-bioB_avg-signal118.332893
Spike_AFFX-r2-Bs-thr_avg-signal44.334061
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1238.457520
Spike_AFFX-r2-Bs-phe_5_signal13.578132
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1865.248169
RawQ2.906309
Spike_AFFX-r2-Bs-lys_5_signal10.211308
Signal(A)5.856712
%A38.882069
Signal(All)157.164948
Corner+Avg:144,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal473.161835
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal17.488781
Spike_AFFX-r2-Ec-bioD_avg-signal1551.852783
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.153881
Spike_AFFX-r2-Bs-lys_avg-signal13.739766
Spike_AFFX-r2-P1-cre_avg-signal5837.674805
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_signal60.921787
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-signal17.791662
Spike_AFFX-r2-Bs-dap_3_signal152.352341
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.506106
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal430.747467
#M448
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.827833
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.098467
Spike_AFFX-r2-Bs-thr_M_signal48.641262
Signal(P)261.089966
Spike_AFFX-r2-Bs-phe_3-5-ratio1.288011
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6361,Count:9
Spike_AFFX-r2-P1-cre_5_signal5100.806641
Spike_AFFX-r2-Bs-phe_M_detectionM
#A8869
Signal(M)22.550138
BackgroundAvg:72.45,Std:0.46,Min:71.5,Max:73.9
Spike_AFFX-r2-Ec-bioC_avg-signal451.954651
Spike_AFFX-r2-Bs-dap_avg-signal100.749077
Spike_AFFX-r2-Bs-dap_3-5-ratio2.694345
Spike_AFFX-r2-Ec-bioB_5_signal112.281837
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.665849
NF1.000000
HZ4
Tau0.015000

Slide: Rasmusson_566-12_ndb1-8.7_Rep4_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 ("Rasmusson_566-12_ndb1-8.7_Rep4_ATH1") was made from "" 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: Rasmusson_566-12_ndb1-8.7_Rep4_ATH1
Organism:
Stock Code:
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:0.801208
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-ratio1.123906
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.177190
Spike_AFFX-r2-Bs-dap_5_signal59.199474
NoiseAvg:2.97,Std:0.08,Min:2.8,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal26.132555
#P13241
Spike_AFFX-r2-Bs-phe_M_signal22.576576
Corner-Avg:8072,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal157.102737
Spike_AFFX-r2-Ec-bioB_3_signal133.193771
Spike_AFFX-r2-Bs-lys_M_signal13.620669
Spike_AFFX-r2-P1-cre_3_signal6562.260742
Spike_AFFX-r2-Bs-lys_3-5-ratio2.240078
Spike_AFFX-r2-Bs-dap_M_signal138.131332
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.535405
Spike_AFFX-r2-Ec-bioB_avg-signal134.480682
Spike_AFFX-r2-Bs-thr_avg-signal60.724155
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1145.683472
Spike_AFFX-r2-Bs-phe_5_signal21.033352
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1912.462036
RawQ2.765354
Spike_AFFX-r2-Bs-lys_5_signal13.671152
Signal(A)6.544359
%A39.912319
Signal(All)159.539001
Corner+Avg:126,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal518.786072
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal31.883062
Spike_AFFX-r2-Ec-bioD_avg-signal1529.072754
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.049103
Spike_AFFX-r2-Bs-lys_avg-signal19.305422
Spike_AFFX-r2-P1-cre_avg-signal6200.528320
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.038579
Spike_AFFX-r2-Bs-thr_3_signal92.389175
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal25.164331
Spike_AFFX-r2-Bs-dap_3_signal156.167282
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.669276
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal550.614624
#M465
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal30.624447
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.942195
Spike_AFFX-r2-Bs-thr_M_signal63.650734
Signal(P)269.517700
Spike_AFFX-r2-Bs-phe_3-5-ratio1.515834
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6331,Count:9
Spike_AFFX-r2-P1-cre_5_signal5838.796387
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9104
Signal(M)23.270672
BackgroundAvg:69.81,Std:0.40,Min:68.8,Max:71.2
Spike_AFFX-r2-Ec-bioC_avg-signal534.700317
Spike_AFFX-r2-Bs-dap_avg-signal117.832695
Spike_AFFX-r2-Bs-dap_3-5-ratio2.637984
Spike_AFFX-r2-Ec-bioB_5_signal113.145546
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.801208
NF1.000000
HZ4
Tau0.015000

Slide: Rasmusson_566-13_ndb1-1.5_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 ("Rasmusson_566-13_ndb1-1.5_Rep1_ATH1") was made from "" 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: Rasmusson_566-13_ndb1-1.5_Rep1_ATH1
Organism:
Stock Code:
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:0.774608
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-ratio1.134585
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.854387
Spike_AFFX-r2-Bs-dap_5_signal43.818443
NoiseAvg:3.66,Std:0.10,Min:3.3,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.459435
#P12932
Spike_AFFX-r2-Bs-phe_M_signal12.003366
Corner-Avg:9097,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal122.467842
Spike_AFFX-r2-Ec-bioB_3_signal107.207291
Spike_AFFX-r2-Bs-lys_M_signal9.569823
Spike_AFFX-r2-P1-cre_3_signal6752.165527
Spike_AFFX-r2-Bs-lys_3-5-ratio36.224453
Spike_AFFX-r2-Bs-dap_M_signal85.964020
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.426563
Spike_AFFX-r2-Ec-bioB_avg-signal118.384583
Spike_AFFX-r2-Bs-thr_avg-signal41.657894
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1310.108887
Spike_AFFX-r2-Bs-phe_5_signal16.588938
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1990.192139
RawQ3.247618
Spike_AFFX-r2-Bs-lys_5_signal0.793574
Signal(A)6.993870
%A41.192459
Signal(All)160.166046
Corner+Avg:144,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal504.097687
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal15.719287
Spike_AFFX-r2-Ec-bioD_avg-signal1650.150513
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P56.694431
Spike_AFFX-r2-Bs-lys_avg-signal15.529284
Spike_AFFX-r2-P1-cre_avg-signal6351.694336
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.113108
Spike_AFFX-r2-Bs-thr_3_signal49.646095
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal14.770531
Spike_AFFX-r2-Bs-dap_3_signal112.806061
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.519104
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal514.352356
#M482
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal36.224453
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.980063
Spike_AFFX-r2-Bs-thr_M_signal54.868156
Signal(P)276.483704
Spike_AFFX-r2-Bs-phe_3-5-ratio0.947576
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5926,Count:9
Spike_AFFX-r2-P1-cre_5_signal5951.222656
Spike_AFFX-r2-Bs-phe_M_detectionM
#A9396
Signal(M)25.281803
BackgroundAvg:81.15,Std:0.88,Min:79.3,Max:82.9
Spike_AFFX-r2-Ec-bioC_avg-signal509.225037
Spike_AFFX-r2-Bs-dap_avg-signal80.862846
Spike_AFFX-r2-Bs-dap_3-5-ratio2.574397
Spike_AFFX-r2-Ec-bioB_5_signal125.478607
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.774608
NF1.000000
HZ4
Tau0.015000

Slide: Rasmusson_566-14_ndb1-1.5_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 ("Rasmusson_566-14_ndb1-1.5_Rep2_ATH1") was made from "" 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: Rasmusson_566-14_ndb1-1.5_Rep2_ATH1
Organism:
Stock Code:
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:0.44801
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-ratio1.224204
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.260451
Spike_AFFX-r2-Bs-dap_5_signal66.952003
NoiseAvg:4.11,Std:0.19,Min:3.8,Max:5.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal28.582220
#P13951
Spike_AFFX-r2-Bs-phe_M_signal20.983944
Corner-Avg:12031,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal125.033737
Spike_AFFX-r2-Ec-bioB_3_signal116.452232
Spike_AFFX-r2-Bs-lys_M_signal9.460357
Spike_AFFX-r2-P1-cre_3_signal5429.724609
Spike_AFFX-r2-Bs-lys_3-5-ratio1.763686
Spike_AFFX-r2-Bs-dap_M_signal129.035980
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.987042
Spike_AFFX-r2-Ec-bioB_avg-signal111.291771
Spike_AFFX-r2-Bs-thr_avg-signal44.185699
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1261.455200
Spike_AFFX-r2-Bs-phe_5_signal19.374277
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1792.696045
RawQ3.434112
Spike_AFFX-r2-Bs-lys_5_signal14.662457
Signal(A)4.407835
%A37.053925
Signal(All)151.613388
Corner+Avg:192,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal423.742920
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.707930
Spike_AFFX-r2-Ec-bioD_avg-signal1527.075684
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.161770
Spike_AFFX-r2-Bs-lys_avg-signal16.660925
Spike_AFFX-r2-P1-cre_avg-signal4932.516602
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.784305
Spike_AFFX-r2-Bs-thr_3_signal56.794060
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-signal20.688715
Spike_AFFX-r2-Bs-dap_3_signal155.562912
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.421133
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal408.369202
#M407
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal25.859962
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.037647
Spike_AFFX-r2-Bs-thr_M_signal47.180820
Signal(P)244.683136
Spike_AFFX-r2-Bs-phe_3-5-ratio1.120451
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8804,Count:9
Spike_AFFX-r2-P1-cre_5_signal4435.309082
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8452
Signal(M)18.358189
BackgroundAvg:91.87,Std:0.82,Min:90.0,Max:93.8
Spike_AFFX-r2-Ec-bioC_avg-signal416.056061
Spike_AFFX-r2-Bs-dap_avg-signal117.183624
Spike_AFFX-r2-Bs-dap_3-5-ratio2.323499
Spike_AFFX-r2-Ec-bioB_5_signal92.389336
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.448010
NF1.000000
HZ4
Tau0.015000

Slide: Rasmusson_566-15_ndb1-1.5_Rep4_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 ("Rasmusson_566-15_ndb1-1.5_Rep4_ATH1") was made from "" 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: Rasmusson_566-15_ndb1-1.5_Rep4_ATH1
Organism:
Stock Code:
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:0.732027
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-ratio1.169869
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.862681
Spike_AFFX-r2-Bs-dap_5_signal60.090500
NoiseAvg:4.18,Std:0.31,Min:3.7,Max:5.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal29.066036
#P12785
Spike_AFFX-r2-Bs-phe_M_signal20.886436
Corner-Avg:9234,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal100.986244
Spike_AFFX-r2-Ec-bioB_3_signal79.685440
Spike_AFFX-r2-Bs-lys_M_signal11.925327
Spike_AFFX-r2-P1-cre_3_signal5384.842285
Spike_AFFX-r2-Bs-lys_3-5-ratio1.531609
Spike_AFFX-r2-Bs-dap_M_signal113.177895
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.444371
Spike_AFFX-r2-Ec-bioB_avg-signal91.013733
Spike_AFFX-r2-Bs-thr_avg-signal55.148273
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal912.819824
Spike_AFFX-r2-Bs-phe_5_signal22.503864
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1592.754150
RawQ3.450640
Spike_AFFX-r2-Bs-lys_5_signal15.749994
Signal(A)7.856737
%A41.775536
Signal(All)156.992737
Corner+Avg:156,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal340.097137
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal32.088356
Spike_AFFX-r2-Ec-bioD_avg-signal1252.786987
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P56.049976
Spike_AFFX-r2-Bs-lys_avg-signal17.266052
Spike_AFFX-r2-P1-cre_avg-signal4993.893555
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.174485
Spike_AFFX-r2-Bs-thr_3_signal71.048164
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal25.159552
Spike_AFFX-r2-Bs-dap_3_signal163.306961
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.744872
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal399.038818
#M496
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.122839
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.852291
Spike_AFFX-r2-Bs-thr_M_signal65.330627
Signal(P)273.262604
Spike_AFFX-r2-Bs-phe_3-5-ratio1.425904
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6057,Count:9
Spike_AFFX-r2-P1-cre_5_signal4602.944336
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9529
Signal(M)25.151741
BackgroundAvg:92.35,Std:0.98,Min:90.4,Max:94.9
Spike_AFFX-r2-Ec-bioC_avg-signal369.567993
Spike_AFFX-r2-Bs-dap_avg-signal112.191795
Spike_AFFX-r2-Bs-dap_3-5-ratio2.717684
Spike_AFFX-r2-Ec-bioB_5_signal92.369507
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.732027
NF1.000000
HZ4
Tau0.015000


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