NASC's International Affymetrix Service

AI logo

NASCArrays

home, selection, spot history, gene swinger, two gene scatterplot, digital northern, bulk gene download, tutorial, help, Affymetrix site, NASC

Experiment: Transcriptional profiling in stem segments of Columbia wild type and the wox4 mutant

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-539

Columbia wild type and wox4 mutant stem segments were analysed for transcriptional profiling

About the Experimenter

Name:Dr Stefanie Suer
Head of Lab Name: Thomas Greb
Lab:
Address:Greb Laboratory, Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences
Dr. Bohr-Gasse 3, Wien, Vienna, , A-1030, AUSTRIA
Postcode:
Country:
 
Telephone Number: 00431790449837

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

About this Experiment

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

Slides in this Experiment

Hybridisation Set: Suer: Transcriptional profiling in stem segments of Columbia wild type and the wox4 mutant

Slide: Suer_539-1_Col base 1_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Suer_539-1_Col base 1_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: Suer_539-1_Col base 1_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
Stratificationafter sowing 3 days 4°C
ProtocolThe plants where grown on soil for 3 weeks under short day conditions, then transferred to single pots and long day conditions.
Plant Spacing40 plants per tray
watertwice weekly
Temperature22.5 °C average, 63 °C day, 21.5 °C night
Humidity63 % average, 63 % day, 59 % night
MediumNone
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Tissue: stem segment at the base
Additional Organism Information:
Sample DescriptionWild type Columbia
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:0.745056
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-ratio1.345114
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.261930
Spike_AFFX-r2-Bs-dap_5_signal180.150742
NoiseAvg:2.57,Std:0.09,Min:2.3,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal42.440849
#P14203
Spike_AFFX-r2-Bs-phe_M_signal61.474777
Corner-Avg:16364,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal87.312447
Spike_AFFX-r2-Ec-bioB_3_signal96.010498
Spike_AFFX-r2-Bs-lys_M_signal49.746323
Spike_AFFX-r2-P1-cre_3_signal4814.295898
Spike_AFFX-r2-Bs-lys_3-5-ratio2.716583
Spike_AFFX-r2-Bs-dap_M_signal321.233185
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.336563
Spike_AFFX-r2-Ec-bioB_avg-signal86.468414
Spike_AFFX-r2-Bs-thr_avg-signal134.647659
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1100.500000
Spike_AFFX-r2-Bs-phe_5_signal76.656410
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1673.293335
RawQ2.348176
Spike_AFFX-r2-Bs-lys_5_signal32.508106
Signal(A)4.721396
%A35.944759
Signal(All)139.147949
Corner+Avg:125,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal245.945129
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal143.291428
Spike_AFFX-r2-Ec-bioD_avg-signal1386.896729
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.266548
Spike_AFFX-r2-Bs-lys_avg-signal56.855129
Spike_AFFX-r2-P1-cre_avg-signal4196.697266
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.788689
Spike_AFFX-r2-Bs-thr_3_signal226.488251
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-signal93.807533
Spike_AFFX-r2-Bs-dap_3_signal723.497253
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.520485
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal199.980484
#M408
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal88.310959
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.229846
Spike_AFFX-r2-Bs-thr_M_signal135.013855
Signal(P)220.253983
Spike_AFFX-r2-Bs-phe_3-5-ratio1.869269
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14514,Count:9
Spike_AFFX-r2-P1-cre_5_signal3579.098145
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8199
Signal(M)17.124577
BackgroundAvg:53.55,Std:0.57,Min:52.3,Max:55.5
Spike_AFFX-r2-Ec-bioC_avg-signal222.962799
Spike_AFFX-r2-Bs-dap_avg-signal408.293732
Spike_AFFX-r2-Bs-dap_3-5-ratio4.016066
Spike_AFFX-r2-Ec-bioB_5_signal76.082298
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.745056
NF1.000000
HZ4
Tau0.015000

Slide: Suer_539-2_Col base 2_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 ("Suer_539-2_Col base 2_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: Suer_539-2_Col base 2_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
Stratificationafter sowing 3 days 4°C
ProtocolThe plants where grown on soil for 3 weeks under short day conditions, then transferred to single pots and long day conditions.
Plant Spacing40 plants per tray
watertwice weekly
Temperature22.5 °C average, 22.5 °C day, 21.5 °C night
Humidity63 % average, 63 % day, 59 % night
MediumNone
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Tissue: stem segment at the base
Additional Organism Information:
Sample DescriptionWild type Columbia
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:0.709519
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-ratio1.345079
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.099669
Spike_AFFX-r2-Bs-dap_5_signal97.036736
NoiseAvg:2.43,Std:0.06,Min:2.2,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_signal28.211168
#P14356
Spike_AFFX-r2-Bs-phe_M_signal65.013153
Corner-Avg:17170,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal107.565643
Spike_AFFX-r2-Ec-bioB_3_signal79.817551
Spike_AFFX-r2-Bs-lys_M_signal41.963810
Spike_AFFX-r2-P1-cre_3_signal5087.406250
Spike_AFFX-r2-Bs-lys_3-5-ratio2.133777
Spike_AFFX-r2-Bs-dap_M_signal349.806854
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.578026
Spike_AFFX-r2-Ec-bioB_avg-signal86.655495
Spike_AFFX-r2-Bs-thr_avg-signal132.996429
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1263.451050
Spike_AFFX-r2-Bs-phe_5_signal67.040077
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1816.065063
RawQ2.191526
Spike_AFFX-r2-Bs-lys_5_signal38.315639
Signal(A)4.191592
%A35.458134
Signal(All)139.773148
Corner+Avg:132,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal227.260208
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal125.847031
Spike_AFFX-r2-Ec-bioD_avg-signal1539.758057
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.937309
Spike_AFFX-r2-Bs-lys_avg-signal54.012157
Spike_AFFX-r2-P1-cre_avg-signal4434.821777
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.604559
Spike_AFFX-r2-Bs-thr_3_signal270.207306
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-signal85.966759
Spike_AFFX-r2-Bs-dap_3_signal630.812073
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.437385
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal196.799744
#M366
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal81.757019
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.154779
Spike_AFFX-r2-Bs-thr_M_signal100.570801
Signal(P)219.316483
Spike_AFFX-r2-Bs-phe_3-5-ratio1.877191
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14871,Count:9
Spike_AFFX-r2-P1-cre_5_signal3782.237305
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8088
Signal(M)15.891411
BackgroundAvg:53.34,Std:0.40,Min:52.3,Max:54.3
Spike_AFFX-r2-Ec-bioC_avg-signal212.029968
Spike_AFFX-r2-Bs-dap_avg-signal359.218536
Spike_AFFX-r2-Bs-dap_3-5-ratio6.500755
Spike_AFFX-r2-Ec-bioB_5_signal72.583282
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.709519
NF1.000000
HZ4
Tau0.015000

Slide: Suer_539-3_Col base 3_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 ("Suer_539-3_Col base 3_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: Suer_539-3_Col base 3_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
Stratificationafter sowing 3 days 4°C
ProtocolThe plants where grown on soil for 3 weeks under short day conditions, then transferred to single pots and long day conditions.
Plant Spacing40 plants per tray
watertwice weekly
Temperature22.5 °C average, 22.5 °C day, 21.5 °C night
Humidity63 % average, 63 % day, 59 % night
MediumNone
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Tissue: stem segment at the base
Additional Organism Information:
Sample DescriptionWild type Columbia
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:0.974455
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-ratio1.233925
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.142519
Spike_AFFX-r2-Bs-dap_5_signal287.256012
NoiseAvg:2.09,Std:0.06,Min:1.9,Max:2.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal57.253853
#P14104
Spike_AFFX-r2-Bs-phe_M_signal96.569687
Corner-Avg:16987,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal159.907333
Spike_AFFX-r2-Ec-bioB_3_signal123.111168
Spike_AFFX-r2-Bs-lys_M_signal51.519047
Spike_AFFX-r2-P1-cre_3_signal6750.990723
Spike_AFFX-r2-Bs-lys_3-5-ratio2.092428
Spike_AFFX-r2-Bs-dap_M_signal552.369446
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.714758
Spike_AFFX-r2-Ec-bioB_avg-signal130.257538
Spike_AFFX-r2-Bs-thr_avg-signal227.150558
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1754.268066
Spike_AFFX-r2-Bs-phe_5_signal117.572701
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2515.632568
RawQ2.089699
Spike_AFFX-r2-Bs-lys_5_signal49.405560
Signal(A)4.569333
%A36.567295
Signal(All)143.416687
Corner+Avg:141,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal316.129761
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal198.064545
Spike_AFFX-r2-Ec-bioD_avg-signal2134.950195
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.832531
Spike_AFFX-r2-Bs-lys_avg-signal68.100739
Spike_AFFX-r2-P1-cre_avg-signal6111.070313
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.600175
Spike_AFFX-r2-Bs-thr_3_signal441.699615
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal137.402298
Spike_AFFX-r2-Bs-dap_3_signal1012.332397
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.434007
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal293.627411
#M365
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal103.377602
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.076636
Spike_AFFX-r2-Bs-thr_M_signal182.498215
Signal(P)228.768097
Spike_AFFX-r2-Bs-phe_3-5-ratio1.684613
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14931,Count:9
Spike_AFFX-r2-P1-cre_5_signal5471.150391
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8341
Signal(M)18.291765
BackgroundAvg:48.75,Std:0.36,Min:47.8,Max:49.5
Spike_AFFX-r2-Ec-bioC_avg-signal304.878601
Spike_AFFX-r2-Bs-dap_avg-signal617.319275
Spike_AFFX-r2-Bs-dap_3-5-ratio3.524147
Spike_AFFX-r2-Ec-bioB_5_signal107.754112
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.974455
NF1.000000
HZ4
Tau0.015000

Slide: Suer_539-4_wox4 base 1_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Suer_539-4_wox4 base 1_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: Suer_539-4_wox4 base 1_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: GK-462G01
Stock Code: N444329
Genetic Background: Columbia-0
Growth Conditions:
Stratificationafter sowing 3 days 4°C
ProtocolThe plants where grown on soil for 3 weeks under short day conditions, then transferred to single pots and long day conditions.
Plant Spacing40 plants per tray
watertwice weekly
Temperature22.5 °C average, 22.5 °C day, 21.5 °C night
Humidity63 % average, 63 % day, 59 % night
MediumNone
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Genetic Variation: T-DNA insertion
Tissue: stem segment at the base
Additional Organism Information:
Sample DescriptionGK-462GO1, wox4 mutant
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:1.011859
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-ratio1.277238
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.211832
Spike_AFFX-r2-Bs-dap_5_signal202.308060
NoiseAvg:2.25,Std:0.12,Min:2.0,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_signal51.778049
#P13327
Spike_AFFX-r2-Bs-phe_M_signal72.097389
Corner-Avg:16271,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal119.156853
Spike_AFFX-r2-Ec-bioB_3_signal103.061745
Spike_AFFX-r2-Bs-lys_M_signal49.692688
Spike_AFFX-r2-P1-cre_3_signal5707.532715
Spike_AFFX-r2-Bs-lys_3-5-ratio2.724183
Spike_AFFX-r2-Bs-dap_M_signal424.812073
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.049773
Spike_AFFX-r2-Ec-bioB_avg-signal102.421600
Spike_AFFX-r2-Bs-thr_avg-signal168.126205
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1532.908203
Spike_AFFX-r2-Bs-phe_5_signal62.811829
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2077.992432
RawQ2.117793
Spike_AFFX-r2-Bs-lys_5_signal35.079296
Signal(A)5.702940
%A39.706268
Signal(All)146.811371
Corner+Avg:135,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal232.187668
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal155.327560
Spike_AFFX-r2-Ec-bioD_avg-signal1805.450317
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.426128
Spike_AFFX-r2-Bs-lys_avg-signal60.111469
Spike_AFFX-r2-P1-cre_avg-signal5088.092773
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.867602
Spike_AFFX-r2-Bs-thr_3_signal313.245453
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-signal96.745598
Spike_AFFX-r2-Bs-dap_3_signal743.413818
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.355588
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal236.258438
#M426
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal95.562424
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.982770
Spike_AFFX-r2-Bs-thr_M_signal139.355103
Signal(P)246.748306
Spike_AFFX-r2-Bs-phe_3-5-ratio2.472903
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14111,Count:9
Spike_AFFX-r2-P1-cre_5_signal4468.652832
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9057
Signal(M)20.424814
BackgroundAvg:51.64,Std:0.77,Min:50.0,Max:54.6
Spike_AFFX-r2-Ec-bioC_avg-signal234.223053
Spike_AFFX-r2-Bs-dap_avg-signal456.844635
Spike_AFFX-r2-Bs-dap_3-5-ratio3.674662
Spike_AFFX-r2-Ec-bioB_5_signal85.046204
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.011859
NF1.000000
HZ4
Tau0.015000

Slide: Suer_539-5_wox4 base 2_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 ("Suer_539-5_wox4 base 2_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: Suer_539-5_wox4 base 2_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: GK-462G01
Stock Code: N444329
Genetic Background: Columbia-0
Growth Conditions:
Stratificationafter sowing 3 days 4°C
ProtocolThe plants where grown on soil for 3 weeks under short day conditions, then transferred to single pots and long day conditions.
Plant Spacing40 plants per tray
watertwice weekly
Temperature22.5 °C average, 22.5 °C day, 21.5 °C night
Humidity63 % average, 63 % day, 59 % night
MediumNone
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Genetic Variation: T-DNA insertion
Tissue: stem segment at the base
Additional Organism Information:
Sample DescriptionGK-462GO1, wox4 mutant
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:0.895284
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-ratio1.345378
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.246393
Spike_AFFX-r2-Bs-dap_5_signal163.681137
NoiseAvg:2.30,Std:0.11,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_signal51.428959
#P13899
Spike_AFFX-r2-Bs-phe_M_signal52.587040
Corner-Avg:16409,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal112.248238
Spike_AFFX-r2-Ec-bioB_3_signal96.832756
Spike_AFFX-r2-Bs-lys_M_signal29.911249
Spike_AFFX-r2-P1-cre_3_signal5652.198730
Spike_AFFX-r2-Bs-lys_3-5-ratio2.096030
Spike_AFFX-r2-Bs-dap_M_signal346.468964
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.209035
Spike_AFFX-r2-Ec-bioB_avg-signal95.590462
Spike_AFFX-r2-Bs-thr_avg-signal113.612572
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1343.430786
Spike_AFFX-r2-Bs-phe_5_signal51.625866
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1787.092773
RawQ2.166749
Spike_AFFX-r2-Bs-lys_5_signal32.890198
Signal(A)4.931428
%A37.299431
Signal(All)141.593643
Corner+Avg:145,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal230.319534
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal107.011192
Spike_AFFX-r2-Ec-bioD_avg-signal1565.261719
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.933800
Spike_AFFX-r2-Bs-lys_avg-signal43.913433
Spike_AFFX-r2-P1-cre_avg-signal4926.697754
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.766769
Spike_AFFX-r2-Bs-thr_3_signal165.037308
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-signal70.408035
Spike_AFFX-r2-Bs-dap_3_signal642.872498
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.330245
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal209.844864
#M403
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal68.938843
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.097571
Spike_AFFX-r2-Bs-thr_M_signal124.371452
Signal(P)228.808090
Spike_AFFX-r2-Bs-phe_3-5-ratio2.072821
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13373,Count:9
Spike_AFFX-r2-P1-cre_5_signal4201.196777
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8508
Signal(M)18.835089
BackgroundAvg:52.35,Std:0.72,Min:50.9,Max:53.7
Spike_AFFX-r2-Ec-bioC_avg-signal220.082199
Spike_AFFX-r2-Bs-dap_avg-signal384.340851
Spike_AFFX-r2-Bs-dap_3-5-ratio3.927591
Spike_AFFX-r2-Ec-bioB_5_signal77.690392
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.895284
NF1.000000
HZ4
Tau0.015000

Slide: Suer_539-6_wox4 base 3_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 ("Suer_539-6_wox4 base 3_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: Suer_539-6_wox4 base 3_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: GK-462G01
Stock Code: N444329
Genetic Background: Columbia-0
Growth Conditions:
Stratificationafter sowing 3 days 4°C
ProtocolThe plants where grown on soil for 3 weeks under short day conditions, then transferred to single pots and long day conditions.
Plant Spacing40 plants per tray
watertwice weekly
Temperature22.5 °C average, 22.5 °C day, 21.5 °C night
Humidity63 % average, 63 % day, 59 % night
MediumNone
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Genetic Variation: T-DNA insertion
Tissue: stem segment at the base
Additional Organism Information:
Sample DescriptionGK-462GO1, wox4 mutant
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:1.129267
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-ratio1.321865
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.208160
Spike_AFFX-r2-Bs-dap_5_signal173.131012
NoiseAvg:2.18,Std:0.07,Min:2.0,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_signal50.772987
#P13444
Spike_AFFX-r2-Bs-phe_M_signal65.296005
Corner-Avg:15136,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal129.857681
Spike_AFFX-r2-Ec-bioB_3_signal97.265953
Spike_AFFX-r2-Bs-lys_M_signal32.054291
Spike_AFFX-r2-P1-cre_3_signal5941.511230
Spike_AFFX-r2-Bs-lys_3-5-ratio2.463889
Spike_AFFX-r2-Bs-dap_M_signal375.515717
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.846372
Spike_AFFX-r2-Ec-bioB_avg-signal102.543724
Spike_AFFX-r2-Bs-thr_avg-signal138.724686
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1304.873413
Spike_AFFX-r2-Bs-phe_5_signal56.662300
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1994.072144
RawQ2.144932
Spike_AFFX-r2-Bs-lys_5_signal36.422096
Signal(A)6.087427
%A39.079350
Signal(All)143.765823
Corner+Avg:204,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal247.897141
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal116.249519
Spike_AFFX-r2-Ec-bioD_avg-signal1649.472778
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.939060
Spike_AFFX-r2-Bs-lys_avg-signal52.738796
Spike_AFFX-r2-P1-cre_avg-signal5218.153320
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.981587
Spike_AFFX-r2-Bs-thr_3_signal246.064774
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-signal79.402611
Spike_AFFX-r2-Bs-dap_3_signal633.103699
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.528173
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal209.809784
#M452
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal89.739998
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.181533
Spike_AFFX-r2-Bs-thr_M_signal119.336281
Signal(P)239.175629
Spike_AFFX-r2-Bs-phe_3-5-ratio2.051620
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12262,Count:9
Spike_AFFX-r2-P1-cre_5_signal4494.795410
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8914
Signal(M)21.145840
BackgroundAvg:51.71,Std:0.47,Min:50.6,Max:52.9
Spike_AFFX-r2-Ec-bioC_avg-signal228.853455
Spike_AFFX-r2-Bs-dap_avg-signal393.916779
Spike_AFFX-r2-Bs-dap_3-5-ratio3.656790
Spike_AFFX-r2-Ec-bioB_5_signal80.507523
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.129267
NF1.000000
HZ4
Tau0.015000

Slide: Suer_539-7_Col stem 1_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Suer_539-7_Col stem 1_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: Suer_539-7_Col stem 1_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
Stratificationafter sowing 3 days 4°C
ProtocolThe plants where grown on soil for 3 weeks under short day conditions, then transferred to single pots and long day conditions.
Plant Spacing40 plants per tray
watertwice weekly
Temperature22.5 °C average, 22.5 °C day, 21.5 °C night
Humidity63 % average, 63 % day, 59 % night
MediumNone
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Tissue: stem segment 1.5 cm above the base
Additional Organism Information:
Sample DescriptionWild type, Columbia
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:0.876328
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-ratio1.350583
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.154652
Spike_AFFX-r2-Bs-dap_5_signal157.466507
NoiseAvg:2.47,Std:0.10,Min:2.2,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal50.595909
#P13976
Spike_AFFX-r2-Bs-phe_M_signal56.611595
Corner-Avg:15469,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal85.015793
Spike_AFFX-r2-Ec-bioB_3_signal70.589592
Spike_AFFX-r2-Bs-lys_M_signal25.731615
Spike_AFFX-r2-P1-cre_3_signal4725.591797
Spike_AFFX-r2-Bs-lys_3-5-ratio2.398027
Spike_AFFX-r2-Bs-dap_M_signal345.086731
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.704466
Spike_AFFX-r2-Ec-bioB_avg-signal72.246773
Spike_AFFX-r2-Bs-thr_avg-signal135.406586
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal980.016479
Spike_AFFX-r2-Bs-phe_5_signal71.608330
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1719.658325
RawQ2.242115
Spike_AFFX-r2-Bs-lys_5_signal35.419487
Signal(A)5.655869
%A36.992546
Signal(All)140.130203
Corner+Avg:197,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal227.585754
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal152.787384
Spike_AFFX-r2-Ec-bioD_avg-signal1349.837402
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.271374
Spike_AFFX-r2-Bs-lys_avg-signal48.695999
Spike_AFFX-r2-P1-cre_avg-signal4112.259766
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.736081
Spike_AFFX-r2-Bs-thr_3_signal238.026749
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-signal93.669106
Spike_AFFX-r2-Bs-dap_3_signal591.670837
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.754724
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal173.241211
#M396
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal84.936897
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.313693
Spike_AFFX-r2-Bs-thr_M_signal117.597084
Signal(P)224.696655
Spike_AFFX-r2-Bs-phe_3-5-ratio2.133654
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14998,Count:9
Spike_AFFX-r2-P1-cre_5_signal3498.927490
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8438
Signal(M)20.921900
BackgroundAvg:55.67,Std:0.57,Min:54.6,Max:57.4
Spike_AFFX-r2-Ec-bioC_avg-signal200.413483
Spike_AFFX-r2-Bs-dap_avg-signal364.741364
Spike_AFFX-r2-Bs-dap_3-5-ratio3.757439
Spike_AFFX-r2-Ec-bioB_5_signal61.134956
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.876328
NF1.000000
HZ4
Tau0.015000

Slide: Suer_539-8_Col stem 2_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 ("Suer_539-8_Col stem 2_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: Suer_539-8_Col stem 2_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
Stratificationafter sowing 3 days 4°C
ProtocolThe plants where grown on soil for 3 weeks under short day conditions, then transferred to single pots and long day conditions.
Plant Spacing40 plants per tray
watertwice weekly
Temperature22.5 °C average, 22.5 °C day, 21.5 °C night
Humidity63 % average, 63 % day, 59 % night
MediumNone
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Tissue: stem segment 1.5 cm above the base
Additional Organism Information:
Sample DescriptionWild type, Columbia
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:0.796015
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-ratio1.440548
Spike_AFFX-r2-Ec-bioB_3-5-ratio2.244492
Spike_AFFX-r2-Bs-dap_5_signal180.007141
NoiseAvg:2.23,Std:0.06,Min:2.1,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal36.532246
#P14479
Spike_AFFX-r2-Bs-phe_M_signal55.296299
Corner-Avg:17868,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal97.376678
Spike_AFFX-r2-Ec-bioB_3_signal91.588974
Spike_AFFX-r2-Bs-lys_M_signal30.756735
Spike_AFFX-r2-P1-cre_3_signal5261.607422
Spike_AFFX-r2-Bs-lys_3-5-ratio2.168510
Spike_AFFX-r2-Bs-dap_M_signal319.317841
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.979035
Spike_AFFX-r2-Ec-bioB_avg-signal76.590584
Spike_AFFX-r2-Bs-thr_avg-signal119.694206
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1186.678223
Spike_AFFX-r2-Bs-phe_5_signal67.701347
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1674.352539
RawQ2.153837
Spike_AFFX-r2-Bs-lys_5_signal27.776159
Signal(A)4.303269
%A35.015343
Signal(All)139.188278
Corner+Avg:145,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal228.021606
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal110.550720
Spike_AFFX-r2-Ec-bioD_avg-signal1430.515381
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.476547
Spike_AFFX-r2-Bs-lys_avg-signal39.588589
Spike_AFFX-r2-P1-cre_avg-signal4457.055664
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.508111
Spike_AFFX-r2-Bs-thr_3_signal218.427567
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-signal77.849457
Spike_AFFX-r2-Bs-dap_3_signal611.783691
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.410957
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal197.990662
#M344
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal60.232876
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.151679
Spike_AFFX-r2-Bs-thr_M_signal104.122795
Signal(P)216.504669
Spike_AFFX-r2-Bs-phe_3-5-ratio1.632918
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14551,Count:9
Spike_AFFX-r2-P1-cre_5_signal3652.503418
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7987
Signal(M)16.696030
BackgroundAvg:54.50,Std:0.38,Min:53.7,Max:55.5
Spike_AFFX-r2-Ec-bioC_avg-signal213.006134
Spike_AFFX-r2-Bs-dap_avg-signal370.369537
Spike_AFFX-r2-Bs-dap_3-5-ratio3.398664
Spike_AFFX-r2-Ec-bioB_5_signal40.806103
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.796015
NF1.000000
HZ4
Tau0.015000

Slide: Suer_539-9_Col stem 3_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 ("Suer_539-9_Col stem 3_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: Suer_539-9_Col stem 3_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
Stratificationafter sowing 3 days 4°C
ProtocolThe plants where grown on soil for 3 weeks under short day conditions, then transferred to single pots and long day conditions.
Plant Spacing40 plants per tray
watertwice weekly
Temperature22.5 °C average, 22.5 °C day, 21.5 °C night
Humidity63 % average, 63 % day, 59 % night
MediumNone
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Tissue: stem segment 1.5 cm above the base
Additional Organism Information:
Sample DescriptionWild type, Columbia
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:0.708368
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-ratio1.328656
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.520387
Spike_AFFX-r2-Bs-dap_5_signal144.489456
NoiseAvg:2.47,Std:0.12,Min:2.1,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_signal50.892281
#P14412
Spike_AFFX-r2-Bs-phe_M_signal56.186214
Corner-Avg:19330,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal106.290497
Spike_AFFX-r2-Ec-bioB_3_signal78.737282
Spike_AFFX-r2-Bs-lys_M_signal31.413761
Spike_AFFX-r2-P1-cre_3_signal4779.094727
Spike_AFFX-r2-Bs-lys_3-5-ratio2.284552
Spike_AFFX-r2-Bs-dap_M_signal294.595367
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.909268
Spike_AFFX-r2-Ec-bioB_avg-signal78.938469
Spike_AFFX-r2-Bs-thr_avg-signal119.082977
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1325.799805
Spike_AFFX-r2-Bs-phe_5_signal49.860279
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1815.947144
RawQ2.148020
Spike_AFFX-r2-Bs-lys_5_signal31.033319
Signal(A)4.281738
%A35.387989
Signal(All)138.789444
Corner+Avg:141,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal237.272766
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal99.679672
Spike_AFFX-r2-Ec-bioD_avg-signal1570.873535
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.182816
Spike_AFFX-r2-Bs-lys_avg-signal44.448105
Spike_AFFX-r2-P1-cre_avg-signal4188.017090
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.429198
Spike_AFFX-r2-Bs-thr_3_signal198.951553
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal68.575386
Spike_AFFX-r2-Bs-dap_3_signal504.668671
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.369699
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal223.558289
#M326
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal70.897232
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.061346
Spike_AFFX-r2-Bs-thr_M_signal107.405098
Signal(P)216.890259
Spike_AFFX-r2-Bs-phe_3-5-ratio1.999180
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15309,Count:9
Spike_AFFX-r2-P1-cre_5_signal3596.939697
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8072
Signal(M)16.572290
BackgroundAvg:76.96,Std:0.72,Min:75.3,Max:79.3
Spike_AFFX-r2-Ec-bioC_avg-signal230.415527
Spike_AFFX-r2-Bs-dap_avg-signal314.584503
Spike_AFFX-r2-Bs-dap_3-5-ratio3.492772
Spike_AFFX-r2-Ec-bioB_5_signal51.787647
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.708368
NF1.000000
HZ4
Tau0.015000

Slide: Suer_539-10_wox4 stem 1_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Suer_539-10_wox4 stem 1_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: Suer_539-10_wox4 stem 1_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: GK-462G01
Stock Code: N444329
Genetic Background: Columbia-0
Growth Conditions:
Stratificationafter sowing 3 days 4°C
ProtocolThe plants where grown on soil for 3 weeks under short day conditions, then transferred to single pots and long day conditions.
Plant Spacing40 plants per tray
watertwice weekly
Temperature22.5 °C average, 22.5 °C day, 21.5 °C night
Humidity63 % average, 63 % day, 59 % night
MediumNone
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Genetic Variation: T-DNA insertion
Tissue: stem segment 1.5 cm above the base
Additional Organism Information:
Sample DescriptionGK-462G01, wox4 mutant
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:0.743962
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-ratio1.361934
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.445564
Spike_AFFX-r2-Bs-dap_5_signal159.756989
NoiseAvg:2.51,Std:0.12,Min:2.3,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal48.229527
#P14086
Spike_AFFX-r2-Bs-phe_M_signal68.064384
Corner-Avg:16635,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal91.782944
Spike_AFFX-r2-Ec-bioB_3_signal81.546059
Spike_AFFX-r2-Bs-lys_M_signal32.327274
Spike_AFFX-r2-P1-cre_3_signal4307.416992
Spike_AFFX-r2-Bs-lys_3-5-ratio2.071561
Spike_AFFX-r2-Bs-dap_M_signal316.960052
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.674446
Spike_AFFX-r2-Ec-bioB_avg-signal76.580078
Spike_AFFX-r2-Bs-thr_avg-signal133.140732
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1038.833862
Spike_AFFX-r2-Bs-phe_5_signal64.566673
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1521.999146
RawQ2.262183
Spike_AFFX-r2-Bs-lys_5_signal33.049503
Signal(A)4.544806
%A36.711967
Signal(All)138.650192
Corner+Avg:133,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal222.214767
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal119.648590
Spike_AFFX-r2-Ec-bioD_avg-signal1280.416504
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.753616
Spike_AFFX-r2-Bs-lys_avg-signal44.613613
Spike_AFFX-r2-P1-cre_avg-signal3735.068848
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.534415
Spike_AFFX-r2-Bs-thr_3_signal225.446320
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal84.093224
Spike_AFFX-r2-Bs-dap_3_signal649.289185
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.465104
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal188.379883
#M350
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal68.464058
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.179610
Spike_AFFX-r2-Bs-thr_M_signal125.746384
Signal(P)221.369858
Spike_AFFX-r2-Bs-phe_3-5-ratio1.853101
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:13867,Count:9
Spike_AFFX-r2-P1-cre_5_signal3162.720947
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8374
Signal(M)18.105352
BackgroundAvg:77.81,Std:0.57,Min:76.9,Max:80.0
Spike_AFFX-r2-Ec-bioC_avg-signal205.297333
Spike_AFFX-r2-Bs-dap_avg-signal375.335419
Spike_AFFX-r2-Bs-dap_3-5-ratio4.064230
Spike_AFFX-r2-Ec-bioB_5_signal56.411228
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.743962
NF1.000000
HZ4
Tau0.015000

Slide: Suer_539-11_wox4 stem 2_Rep_2_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 ("Suer_539-11_wox4 stem 2_Rep_2_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: Suer_539-11_wox4 stem 2_Rep_2_ATH1
Organism: Arabidopsis thaliana
Alias: GK-462G01
Stock Code: N444329
Genetic Background: Columbia-0
Growth Conditions:
Stratificationafter sowing 3 days 4°C
ProtocolThe plants where grown on soil for 3 weeks under short day conditions, then transferred to single pots and long day conditions.
Plant Spacing40 plants per tray
watertwice weekly
Temperature22.5 °C average, 22.5 °C day, 21.5 °C night
Humidity63 % average, 63 % day, 59 % night
MediumNone
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Genetic Variation: T-DNA insertion
Tissue: stem segment 1.5 cm above the base
Additional Organism Information:
Sample DescriptionGK-462G01, wox4 mutant
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:0.71261
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-ratio1.225295
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.398156
Spike_AFFX-r2-Bs-dap_5_signal149.746292
NoiseAvg:2.66,Std:0.07,Min:2.4,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal49.052063
#P14128
Spike_AFFX-r2-Bs-phe_M_signal64.018578
Corner-Avg:18011,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal97.724998
Spike_AFFX-r2-Ec-bioB_3_signal89.216988
Spike_AFFX-r2-Bs-lys_M_signal36.558388
Spike_AFFX-r2-P1-cre_3_signal4384.425781
Spike_AFFX-r2-Bs-lys_3-5-ratio2.751408
Spike_AFFX-r2-Bs-dap_M_signal329.171722
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.826491
Spike_AFFX-r2-Ec-bioB_avg-signal83.584152
Spike_AFFX-r2-Bs-thr_avg-signal140.609970
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1149.118042
Spike_AFFX-r2-Bs-phe_5_signal62.577274
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1764.763550
RawQ2.378955
Spike_AFFX-r2-Bs-lys_5_signal30.939457
Signal(A)4.557716
%A36.540989
Signal(All)138.279633
Corner+Avg:148,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal207.483200
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal108.381157
Spike_AFFX-r2-Ec-bioD_avg-signal1456.940796
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.937748
Spike_AFFX-r2-Bs-lys_avg-signal50.874973
Spike_AFFX-r2-P1-cre_avg-signal3981.343750
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.521263
Spike_AFFX-r2-Bs-thr_3_signal236.749329
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal78.325668
Spike_AFFX-r2-Bs-dap_3_signal577.419556
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.535755
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal216.114838
#M347
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal85.127075
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.960060
Spike_AFFX-r2-Bs-thr_M_signal136.028503
Signal(P)220.128662
Spike_AFFX-r2-Bs-phe_3-5-ratio1.731957
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15488,Count:9
Spike_AFFX-r2-P1-cre_5_signal3578.261475
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8335
Signal(M)17.844931
BackgroundAvg:84.41,Std:0.47,Min:82.9,Max:85.5
Spike_AFFX-r2-Ec-bioC_avg-signal211.799011
Spike_AFFX-r2-Bs-dap_avg-signal352.112549
Spike_AFFX-r2-Bs-dap_3-5-ratio3.855986
Spike_AFFX-r2-Ec-bioB_5_signal63.810471
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.712610
NF1.000000
HZ4
Tau0.015000

Slide: Suer_539-12_wox4 stem 3_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 ("Suer_539-12_wox4 stem 3_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: Suer_539-12_wox4 stem 3_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: GK-462G01
Stock Code: N444329
Genetic Background: Columbia-0
Growth Conditions:
Stratificationafter sowing 3 days 4°C
ProtocolThe plants where grown on soil for 3 weeks under short day conditions, then transferred to single pots and long day conditions.
Plant Spacing40 plants per tray
watertwice weekly
Temperature22.5 °C average, 22.5 °C day, 21.5 °C night
Humidity63 % average, 63 % day, 59 % night
MediumNone
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Genetic Variation: T-DNA insertion
Tissue: stem segment 1.5 cm above the base
Additional Organism Information:
Sample DescriptionGK-462G01, wox4 mutant
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:0.683724
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-ratio1.260435
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.254683
Spike_AFFX-r2-Bs-dap_5_signal117.521057
NoiseAvg:2.69,Std:0.14,Min:2.4,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_signal41.284676
#P14042
Spike_AFFX-r2-Bs-phe_M_signal40.628822
Corner-Avg:17273,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal84.971893
Spike_AFFX-r2-Ec-bioB_3_signal79.121979
Spike_AFFX-r2-Bs-lys_M_signal29.640728
Spike_AFFX-r2-P1-cre_3_signal3919.516113
Spike_AFFX-r2-Bs-lys_3-5-ratio2.043499
Spike_AFFX-r2-Bs-dap_M_signal258.573456
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.331758
Spike_AFFX-r2-Ec-bioB_avg-signal75.718407
Spike_AFFX-r2-Bs-thr_avg-signal90.213776
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal871.165466
Spike_AFFX-r2-Bs-phe_5_signal36.989544
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1523.853394
RawQ2.230408
Spike_AFFX-r2-Bs-lys_5_signal29.976967
Signal(A)4.981346
%A36.847874
Signal(All)138.210342
Corner+Avg:136,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal220.027222
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal95.573723
Spike_AFFX-r2-Ec-bioD_avg-signal1197.509399
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.560719
Spike_AFFX-r2-Bs-lys_avg-signal40.291866
Spike_AFFX-r2-P1-cre_avg-signal3514.584961
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.591407
Spike_AFFX-r2-Bs-thr_3_signal137.550568
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-signal57.730698
Spike_AFFX-r2-Bs-dap_3_signal461.051697
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.749212
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal189.639664
#M363
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal61.257908
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.160238
Spike_AFFX-r2-Bs-thr_M_signal91.806091
Signal(P)221.032913
Spike_AFFX-r2-Bs-phe_3-5-ratio2.583804
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16483,Count:9
Spike_AFFX-r2-P1-cre_5_signal3109.654053
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8405
Signal(M)19.188299
BackgroundAvg:81.35,Std:0.74,Min:79.9,Max:84.9
Spike_AFFX-r2-Ec-bioC_avg-signal204.833435
Spike_AFFX-r2-Bs-dap_avg-signal279.048737
Spike_AFFX-r2-Bs-dap_3-5-ratio3.923141
Spike_AFFX-r2-Ec-bioB_5_signal63.061352
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.683724
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team