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Experiment: elo3/WT

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-613

We want to study the influnce of an elo3 deletion on the transcriptome of Arabidopsis thaliana. The samples are whole plant samples, RNA was extracted using the Trizol-Methode followed by RNA cleanup using RNeasy columes.

About the Experimenter

Name:Dr Lars Fichtner
Head of Lab Name:Prof, Dr Karin Breunig
Lab:
Address:Martin-Luther Universitaet
Institute of genetics
Weinbergweg 10
Halle (Saale)
Postcode: D-06099
Country: Germany
 
Telephone Number: 00493455526322

All of the data available in this website/database is free, and you are free to do whatever you please with it. If you intend to publish work based on any of this data, please acknowledge us, contact the experimenter above, and either acknowledge them or use them as co-authors in the work.

About this Experiment

Experiment Type: genetic_modification_design
Number of Slides:6
 
Experimental Parameters:
parametergene_knock_out
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Fichtner: elo3/WT

Slide: Fichtner_613-1_Col_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 ("Fichtner_613-1_Col_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: Fichtner_613-1_Col_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: GK-636H02
Stock Code: N461046
Growth Conditions:
LocationGreenhouse
Humidity (average)60%
Temperature(average)19oC
Mediumcommercial soil
Developmental Stage:
Developmental stage4 months
Tissue: Whole plant
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.799303
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-ratio1.235424
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.437990
Spike_AFFX-r2-Bs-dap_5_signal77.059013
NoiseAvg:2.32,Std:0.06,Min:2.1,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal25.304657
#P14455
Spike_AFFX-r2-Bs-phe_M_signal66.592247
Corner-Avg:12343,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal105.787926
Spike_AFFX-r2-Ec-bioB_3_signal90.749023
Spike_AFFX-r2-Bs-lys_M_signal35.889206
Spike_AFFX-r2-P1-cre_3_signal4810.999023
Spike_AFFX-r2-Bs-lys_3-5-ratio2.260372
Spike_AFFX-r2-Bs-dap_M_signal325.868866
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.446980
Spike_AFFX-r2-Ec-bioB_avg-signal86.548401
Spike_AFFX-r2-Bs-thr_avg-signal131.357620
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal799.739441
Spike_AFFX-r2-Bs-phe_5_signal92.120605
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1265.952637
RawQ2.103827
Spike_AFFX-r2-Bs-lys_5_signal36.679222
Signal(A)5.223408
%A34.616398
Signal(All)145.425537
Corner+Avg:99,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal269.181366
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal228.632370
Spike_AFFX-r2-Ec-bioD_avg-signal1032.846069
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.371330
Spike_AFFX-r2-Bs-lys_avg-signal51.825710
Spike_AFFX-r2-P1-cre_avg-signal4352.604492
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.012275
Spike_AFFX-r2-Bs-thr_3_signal264.357239
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-signal129.115067
Spike_AFFX-r2-Bs-dap_3_signal583.185608
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.582956
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal196.141113
#M459
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal82.908699
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.372386
Spike_AFFX-r2-Bs-thr_M_signal104.410965
Signal(P)226.058105
Spike_AFFX-r2-Bs-phe_3-5-ratio2.481881
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9986,Count:9
Spike_AFFX-r2-P1-cre_5_signal3894.209717
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7896
Signal(M)17.957474
BackgroundAvg:49.39,Std:0.39,Min:48.3,Max:50.5
Spike_AFFX-r2-Ec-bioC_avg-signal232.661240
Spike_AFFX-r2-Bs-dap_avg-signal328.704498
Spike_AFFX-r2-Bs-dap_3-5-ratio7.568039
Spike_AFFX-r2-Ec-bioB_5_signal63.108250
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.799303
NF1.000000
HZ4
Tau0.015000

Slide: Fichtner_613-2_Col_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Fichtner_613-2_Col_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: Fichtner_613-2_Col_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: GK-636H02
Stock Code: N461046
Growth Conditions:
LocationGreenhouse
Humidity (average)60%
Temperature(average)19oC
Mediumcommercial soil
Developmental Stage:
Developmental stage4 months
Tissue: Whole plant
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.585802
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-ratio1.329693
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.395247
Spike_AFFX-r2-Bs-dap_5_signal59.416676
NoiseAvg:2.26,Std:0.10,Min:1.8,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal19.563011
#P15189
Spike_AFFX-r2-Bs-phe_M_signal75.406044
Corner-Avg:13513,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal88.111702
Spike_AFFX-r2-Ec-bioB_3_signal80.409851
Spike_AFFX-r2-Bs-lys_M_signal34.505970
Spike_AFFX-r2-P1-cre_3_signal5252.051270
Spike_AFFX-r2-Bs-lys_3-5-ratio2.035196
Spike_AFFX-r2-Bs-dap_M_signal360.987152
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio15.389974
Spike_AFFX-r2-Ec-bioB_avg-signal75.384270
Spike_AFFX-r2-Bs-thr_avg-signal138.644440
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal973.146118
Spike_AFFX-r2-Bs-phe_5_signal73.573387
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1423.155151
RawQ1.996946
Spike_AFFX-r2-Bs-lys_5_signal38.893055
Signal(A)3.642353
%A31.793074
Signal(All)144.384369
Corner+Avg:109,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal249.783554
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal176.988403
Spike_AFFX-r2-Ec-bioD_avg-signal1198.150635
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.589218
Spike_AFFX-r2-Bs-lys_avg-signal50.851337
Spike_AFFX-r2-P1-cre_avg-signal4600.937500
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.617712
Spike_AFFX-r2-Bs-thr_3_signal301.074219
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal108.655945
Spike_AFFX-r2-Bs-dap_3_signal764.157043
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.462427
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal234.738907
#M369
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal79.154999
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.064091
Spike_AFFX-r2-Bs-thr_M_signal95.296082
Signal(P)214.735168
Spike_AFFX-r2-Bs-phe_3-5-ratio2.405604
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10530,Count:9
Spike_AFFX-r2-P1-cre_5_signal3949.823730
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7252
Signal(M)14.581844
BackgroundAvg:49.33,Std:0.40,Min:48.1,Max:50.6
Spike_AFFX-r2-Ec-bioC_avg-signal242.261230
Spike_AFFX-r2-Bs-dap_avg-signal394.853607
Spike_AFFX-r2-Bs-dap_3-5-ratio12.860986
Spike_AFFX-r2-Ec-bioB_5_signal57.631260
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.585802
NF1.000000
HZ4
Tau0.015000

Slide: Fichtner_613-3_Col_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Fichtner_613-3_Col_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Fichtner_613-3_Col_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: GK-636H02
Stock Code: N461046
Growth Conditions:
LocationGreenhouse
Humidity (average)60%
Temperature(average)19oC
Mediumcommercial soil
Developmental Stage:
Developmental stage4 months
Tissue: Whole plant
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.939315
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-ratio1.172557
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.213164
Spike_AFFX-r2-Bs-dap_5_signal77.233223
NoiseAvg:2.18,Std:0.09,Min:1.9,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal27.309210
#P14505
Spike_AFFX-r2-Bs-phe_M_signal73.157394
Corner-Avg:11770,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal98.961945
Spike_AFFX-r2-Ec-bioB_3_signal76.851395
Spike_AFFX-r2-Bs-lys_M_signal41.322811
Spike_AFFX-r2-P1-cre_3_signal5402.660156
Spike_AFFX-r2-Bs-lys_3-5-ratio2.295234
Spike_AFFX-r2-Bs-dap_M_signal339.980133
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.488363
Spike_AFFX-r2-Ec-bioB_avg-signal79.720406
Spike_AFFX-r2-Bs-thr_avg-signal156.453934
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal821.513489
Spike_AFFX-r2-Bs-phe_5_signal67.763420
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1512.637939
RawQ2.031224
Spike_AFFX-r2-Bs-lys_5_signal42.100845
Signal(A)5.194977
%A34.498028
Signal(All)145.239471
Corner+Avg:101,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal273.400940
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal153.738144
Spike_AFFX-r2-Ec-bioD_avg-signal1167.075684
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.590530
Spike_AFFX-r2-Bs-lys_avg-signal60.018314
Spike_AFFX-r2-P1-cre_avg-signal5005.124023
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.911442
Spike_AFFX-r2-Bs-thr_3_signal313.738129
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-signal98.219658
Spike_AFFX-r2-Bs-dap_3_signal755.589905
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.841282
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal204.483688
#M436
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal96.631294
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.337031
Spike_AFFX-r2-Bs-thr_M_signal128.314468
Signal(P)225.036072
Spike_AFFX-r2-Bs-phe_3-5-ratio2.268748
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10012,Count:9
Spike_AFFX-r2-P1-cre_5_signal4607.588379
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7869
Signal(M)18.084278
BackgroundAvg:49.34,Std:0.33,Min:48.5,Max:50.2
Spike_AFFX-r2-Ec-bioC_avg-signal238.942322
Spike_AFFX-r2-Bs-dap_avg-signal390.934448
Spike_AFFX-r2-Bs-dap_3-5-ratio9.783224
Spike_AFFX-r2-Ec-bioB_5_signal63.347878
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.939315
NF1.000000
HZ4
Tau0.015000

Slide: Fichtner_613-4_elo3_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 ("Fichtner_613-4_elo3_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: Fichtner_613-4_elo3_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: GK-636H02
Stock Code: N461046
Growth Conditions:
LocationGreenhouse
Humidity (average)60%
Temperature(average)19oC
Mediumcommercial soil
Developmental Stage:
Developmental stage4 months
Tissue: Whole plant
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.582221
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-ratio1.263835
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.230925
Spike_AFFX-r2-Bs-dap_5_signal86.869659
NoiseAvg:2.48,Std:0.05,Min:2.4,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.973040
#P14491
Spike_AFFX-r2-Bs-phe_M_signal89.065338
Corner-Avg:13661,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal101.251556
Spike_AFFX-r2-Ec-bioB_3_signal73.266869
Spike_AFFX-r2-Bs-lys_M_signal48.244118
Spike_AFFX-r2-P1-cre_3_signal5134.922852
Spike_AFFX-r2-Bs-lys_3-5-ratio1.581482
Spike_AFFX-r2-Bs-dap_M_signal381.689453
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio21.791529
Spike_AFFX-r2-Ec-bioB_avg-signal78.013405
Spike_AFFX-r2-Bs-thr_avg-signal200.671021
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal988.905396
Spike_AFFX-r2-Bs-phe_5_signal102.381554
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1383.582886
RawQ2.332551
Spike_AFFX-r2-Bs-lys_5_signal52.023037
Signal(A)3.582493
%A34.971504
Signal(All)144.661423
Corner+Avg:117,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal231.637817
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal207.656754
Spike_AFFX-r2-Ec-bioD_avg-signal1186.244141
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.529156
Spike_AFFX-r2-Bs-lys_avg-signal60.846878
Spike_AFFX-r2-P1-cre_avg-signal4598.946777
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.499342
Spike_AFFX-r2-Bs-thr_3_signal457.034576
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-signal133.034561
Spike_AFFX-r2-Bs-dap_3_signal854.000549
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.399105
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal231.128479
#M342
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal82.273476
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.002204
Spike_AFFX-r2-Bs-thr_M_signal124.005486
Signal(P)225.402618
Spike_AFFX-r2-Bs-phe_3-5-ratio2.028263
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10758,Count:9
Spike_AFFX-r2-P1-cre_5_signal4062.970703
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7977
Signal(M)14.153149
BackgroundAvg:55.90,Std:0.61,Min:54.2,Max:57.4
Spike_AFFX-r2-Ec-bioC_avg-signal231.383148
Spike_AFFX-r2-Bs-dap_avg-signal440.853180
Spike_AFFX-r2-Bs-dap_3-5-ratio9.830827
Spike_AFFX-r2-Ec-bioB_5_signal59.521790
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.582221
NF1.000000
HZ4
Tau0.015000

Slide: Fichtner_613-5_elo3_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 ("Fichtner_613-5_elo3_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: Fichtner_613-5_elo3_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: GK-636H02
Stock Code: N461046
Growth Conditions:
LocationGreenhouse
Humidity (average)60%
Temperature(average)19oC
Mediumcommercial soil
Developmental Stage:
Developmental stage4 months
Tissue: Whole plant
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.518753
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-ratio1.232271
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.171227
Spike_AFFX-r2-Bs-dap_5_signal79.789871
NoiseAvg:2.48,Std:0.08,Min:2.3,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal22.314997
#P14255
Spike_AFFX-r2-Bs-phe_M_signal70.550568
Corner-Avg:13343,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal82.763947
Spike_AFFX-r2-Ec-bioB_3_signal78.074280
Spike_AFFX-r2-Bs-lys_M_signal50.963459
Spike_AFFX-r2-P1-cre_3_signal4323.353516
Spike_AFFX-r2-Bs-lys_3-5-ratio1.573736
Spike_AFFX-r2-Bs-dap_M_signal377.552704
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio12.845795
Spike_AFFX-r2-Ec-bioB_avg-signal75.832817
Spike_AFFX-r2-Bs-thr_avg-signal140.651840
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal762.970337
Spike_AFFX-r2-Bs-phe_5_signal70.869301
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1243.084473
RawQ2.210926
Spike_AFFX-r2-Bs-lys_5_signal51.874947
Signal(A)3.351927
%A35.826393
Signal(All)141.855453
Corner+Avg:109,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal268.765045
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal196.517746
Spike_AFFX-r2-Ec-bioD_avg-signal1003.027405
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.494518
Spike_AFFX-r2-Bs-lys_avg-signal61.491955
Spike_AFFX-r2-P1-cre_avg-signal3915.897949
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.679088
Spike_AFFX-r2-Bs-thr_3_signal286.653870
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-signal112.645866
Spike_AFFX-r2-Bs-dap_3_signal809.884949
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.629270
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal202.101257
#M383
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal81.637459
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.329853
Spike_AFFX-r2-Bs-thr_M_signal112.986626
Signal(P)224.739761
Spike_AFFX-r2-Bs-phe_3-5-ratio2.772960
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11566,Count:9
Spike_AFFX-r2-P1-cre_5_signal3508.442383
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8172
Signal(M)12.182368
BackgroundAvg:53.27,Std:1.04,Min:50.8,Max:55.4
Spike_AFFX-r2-Ec-bioC_avg-signal235.433151
Spike_AFFX-r2-Bs-dap_avg-signal422.409180
Spike_AFFX-r2-Bs-dap_3-5-ratio10.150223
Spike_AFFX-r2-Ec-bioB_5_signal66.660225
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.518753
NF1.000000
HZ4
Tau0.015000

Slide: Fichtner_613-6_elo3_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Fichtner_613-6_elo3_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: Fichtner_613-6_elo3_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: GK-636H02
Stock Code: N461046
Growth Conditions:
LocationGreenhouse
Humidity (average)60%
Temperature(average)19oC
Mediumcommercial soil
Developmental Stage:
Developmental stage4 months
Tissue: Whole plant
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.830389
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-ratio1.168042
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.922367
Spike_AFFX-r2-Bs-dap_5_signal75.129021
NoiseAvg:2.31,Std:0.07,Min:2.1,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.188757
#P14012
Spike_AFFX-r2-Bs-phe_M_signal61.335892
Corner-Avg:11617,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal98.192062
Spike_AFFX-r2-Ec-bioB_3_signal75.472054
Spike_AFFX-r2-Bs-lys_M_signal46.658985
Spike_AFFX-r2-P1-cre_3_signal4848.955078
Spike_AFFX-r2-Bs-lys_3-5-ratio2.797663
Spike_AFFX-r2-Bs-dap_M_signal302.643707
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio17.097704
Spike_AFFX-r2-Ec-bioB_avg-signal85.162804
Spike_AFFX-r2-Bs-thr_avg-signal162.080643
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal881.682373
Spike_AFFX-r2-Bs-phe_5_signal74.936104
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1320.908325
RawQ2.155289
Spike_AFFX-r2-Bs-lys_5_signal36.172169
Signal(A)4.926732
%A36.869793
Signal(All)144.294907
Corner+Avg:92,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal325.964752
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal192.207596
Spike_AFFX-r2-Ec-bioD_avg-signal1101.295410
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.429199
Spike_AFFX-r2-Bs-lys_avg-signal61.342899
Spike_AFFX-r2-P1-cre_avg-signal4500.153809
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.701008
Spike_AFFX-r2-Bs-thr_3_signal345.181396
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-signal109.493195
Spike_AFFX-r2-Bs-dap_3_signal727.482910
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.498168
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal237.145050
#M388
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal101.197556
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.374537
Spike_AFFX-r2-Bs-thr_M_signal120.871803
Signal(P)231.464447
Spike_AFFX-r2-Bs-phe_3-5-ratio2.564953
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10304,Count:9
Spike_AFFX-r2-P1-cre_5_signal4151.352539
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8410
Signal(M)17.147781
BackgroundAvg:51.65,Std:0.91,Min:49.7,Max:53.7
Spike_AFFX-r2-Ec-bioC_avg-signal281.554901
Spike_AFFX-r2-Bs-dap_avg-signal368.418549
Spike_AFFX-r2-Bs-dap_3-5-ratio9.683114
Spike_AFFX-r2-Ec-bioB_5_signal81.824287
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.830389
NF1.000000
HZ4
Tau0.015000


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