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Experiment: ABCG37 expression profiling

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-623

Root-specific expression profiling of gain- and loss-of-function mutants in response to indole-3-propionic acid (7d-old, 1h 5 µM IPA)

About the Experimenter

Name: Marcel Quint
Head of Lab Name: Marcel Quint
Lab:
Address:Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry
Weinberg 3 , Halle, Sachsen-Anhalt, 06120, GERMANY
Postcode: 06120
Country: GERMANY
 
Telephone Number: +49-345-55821480
Fax Number: +49-345-5582-1409

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

About this Experiment

Experiment Type: genetic_modification
Number of Slides:18
 
Experimental Parameters:
parametergenetic_modification
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Quint: ABCG37 expression profiling

Slide: Quint_623-1_pdr9-2-mock-1h_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 ("Quint_623-1_pdr9-2-mock-1h_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: Quint_623-1_pdr9-2-mock-1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_050885 (L) (N) (homozygous)
Stock Code: CS859461
Genetic Background: Col-0 (Columbia, N60000)
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA Insertion
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with mock ( 50 ml liquid ATS + 0.1 % Ethanol) for 1 h in the dark. After removal of the liquid medium, roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.35451
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-ratio1.191843
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.839844
Spike_AFFX-r2-Bs-dap_5_signal15.641960
NoiseAvg:3.83,Std:0.11,Min:3.4,Max:4.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.017880
#P15295
Spike_AFFX-r2-Bs-phe_M_signal19.654472
Corner-Avg:13640,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal8.249203
Spike_AFFX-r2-Ec-bioB_3_signal8.300582
Spike_AFFX-r2-Bs-lys_M_signal11.339231
Spike_AFFX-r2-P1-cre_3_signal2851.389160
Spike_AFFX-r2-Bs-lys_3-5-ratio1.688342
Spike_AFFX-r2-Bs-dap_M_signal104.272919
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.449922
Spike_AFFX-r2-Ec-bioB_avg-signal7.020452
Spike_AFFX-r2-Bs-thr_avg-signal23.366278
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal529.201416
Spike_AFFX-r2-Bs-phe_5_signal15.147893
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal746.991272
RawQ3.003181
Spike_AFFX-r2-Bs-lys_5_signal17.603340
Signal(A)3.929831
%A31.148619
Signal(All)132.166824
Corner+Avg:235,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal146.091751
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal32.930447
Spike_AFFX-r2-Ec-bioD_avg-signal638.096313
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.053925
Spike_AFFX-r2-Bs-lys_avg-signal19.554342
Spike_AFFX-r2-P1-cre_avg-signal2621.905029
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.797457
Spike_AFFX-r2-Bs-thr_3_signal47.418571
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal22.577604
Spike_AFFX-r2-Bs-dap_3_signal195.712173
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.411544
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal125.301849
#M410
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal29.720455
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.165919
Spike_AFFX-r2-Bs-thr_M_signal17.662376
Signal(P)194.897507
Spike_AFFX-r2-Bs-phe_3-5-ratio2.173929
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12271,Count:9
Spike_AFFX-r2-P1-cre_5_signal2392.420898
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7105
Signal(M)14.260109
BackgroundAvg:71.37,Std:0.75,Min:69.6,Max:72.8
Spike_AFFX-r2-Ec-bioC_avg-signal135.696808
Spike_AFFX-r2-Bs-dap_avg-signal105.209023
Spike_AFFX-r2-Bs-dap_3-5-ratio12.511998
Spike_AFFX-r2-Ec-bioB_5_signal4.511569
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.354510
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-2_pdr9-2-mock-1h_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 ("Quint_623-2_pdr9-2-mock-1h_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: Quint_623-2_pdr9-2-mock-1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_050885 (L) (N) (homozygous)
Stock Code: CS859461
Genetic Background: Col-0 (Columbia, N60000)
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA Insertion
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with mock ( 50 ml liquid ATS + 0.1 % Ethanol) for 1 h in the dark. After removal of the liquid medium, roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.366036
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-ratio1.214680
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.533713
Spike_AFFX-r2-Bs-dap_5_signal25.370359
NoiseAvg:3.32,Std:0.08,Min:3.0,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal3.119982
#P15405
Spike_AFFX-r2-Bs-phe_M_signal12.540180
Corner-Avg:8223,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal8.466455
Spike_AFFX-r2-Ec-bioB_3_signal7.088489
Spike_AFFX-r2-Bs-lys_M_signal14.986613
Spike_AFFX-r2-P1-cre_3_signal3179.713867
Spike_AFFX-r2-Bs-lys_3-5-ratio3.129913
Spike_AFFX-r2-Bs-dap_M_signal116.578323
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio15.997304
Spike_AFFX-r2-Ec-bioB_avg-signal9.612133
Spike_AFFX-r2-Bs-thr_avg-signal26.767733
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal605.744080
Spike_AFFX-r2-Bs-phe_5_signal18.648287
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal887.152893
RawQ2.783849
Spike_AFFX-r2-Bs-lys_5_signal8.819489
Signal(A)3.229510
%A30.894344
Signal(All)132.592789
Corner+Avg:159,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal184.257797
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal27.886614
Spike_AFFX-r2-Ec-bioD_avg-signal746.448486
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.536171
Spike_AFFX-r2-Bs-lys_avg-signal17.136778
Spike_AFFX-r2-P1-cre_avg-signal2898.725586
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.569487
Spike_AFFX-r2-Bs-thr_3_signal49.911301
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-signal19.691694
Spike_AFFX-r2-Bs-dap_3_signal227.094040
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.464567
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal161.839874
#M358
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.604231
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.138519
Spike_AFFX-r2-Bs-thr_M_signal27.271919
Signal(P)194.563126
Spike_AFFX-r2-Bs-phe_3-5-ratio1.495398
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6842,Count:9
Spike_AFFX-r2-P1-cre_5_signal2617.737061
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7047
Signal(M)12.397442
BackgroundAvg:65.88,Std:0.47,Min:64.5,Max:67.2
Spike_AFFX-r2-Ec-bioC_avg-signal173.048828
Spike_AFFX-r2-Bs-dap_avg-signal123.014244
Spike_AFFX-r2-Bs-dap_3-5-ratio8.951156
Spike_AFFX-r2-Ec-bioB_5_signal13.281456
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.366036
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-3_pdr9-2-mock-1h_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 ("Quint_623-3_pdr9-2-mock-1h_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: Quint_623-3_pdr9-2-mock-1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_050885 (L) (N) (homozygous)
Stock Code: CS859461
Genetic Background: Col-0 (Columbia, N60000)
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA Insertion
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with mock ( 50 ml liquid ATS + 0.1 % Ethanol) for 1 h in the dark. After removal of the liquid medium, roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.302227
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-ratio1.119023
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.621292
Spike_AFFX-r2-Bs-dap_5_signal12.405515
NoiseAvg:4.17,Std:0.21,Min:3.7,Max:5.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal3.391577
#P15420
Spike_AFFX-r2-Bs-phe_M_signal13.845429
Corner-Avg:12516,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal9.467414
Spike_AFFX-r2-Ec-bioB_3_signal4.369612
Spike_AFFX-r2-Bs-lys_M_signal10.528022
Spike_AFFX-r2-P1-cre_3_signal2662.532471
Spike_AFFX-r2-Bs-lys_3-5-ratio2.507443
Spike_AFFX-r2-Bs-dap_M_signal73.923691
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.711991
Spike_AFFX-r2-Ec-bioB_avg-signal6.956710
Spike_AFFX-r2-Bs-thr_avg-signal17.044157
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal563.140198
Spike_AFFX-r2-Bs-phe_5_signal12.629905
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal779.552307
RawQ3.142939
Spike_AFFX-r2-Bs-lys_5_signal8.526689
Signal(A)3.371536
%A31.003946
Signal(All)132.539322
Corner+Avg:219,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal149.328796
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal23.194696
Spike_AFFX-r2-Ec-bioD_avg-signal671.346252
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.601929
Spike_AFFX-r2-Bs-lys_avg-signal13.478299
Spike_AFFX-r2-P1-cre_avg-signal2520.934082
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.394125
Spike_AFFX-r2-Bs-thr_3_signal29.547386
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-signal16.556677
Spike_AFFX-r2-Bs-dap_3_signal166.300064
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.384295
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal149.865173
#M318
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.380188
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.996421
Spike_AFFX-r2-Bs-thr_M_signal18.193506
Signal(P)194.243195
Spike_AFFX-r2-Bs-phe_3-5-ratio1.836490
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11424,Count:9
Spike_AFFX-r2-P1-cre_5_signal2379.335938
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7072
Signal(M)13.044879
BackgroundAvg:78.50,Std:1.27,Min:73.9,Max:80.7
Spike_AFFX-r2-Ec-bioC_avg-signal149.596985
Spike_AFFX-r2-Bs-dap_avg-signal84.209755
Spike_AFFX-r2-Bs-dap_3-5-ratio13.405334
Spike_AFFX-r2-Ec-bioB_5_signal7.033104
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.302227
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-4_Col-0-mock-1h_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 ("Quint_623-4_Col-0-mock-1h_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: Quint_623-4_Col-0-mock-1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with mock (liquid ATS medium + 0.1% Ethanol) for 1 h in the dark before roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.479832
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-ratio1.069631
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.752663
Spike_AFFX-r2-Bs-dap_5_signal53.209023
NoiseAvg:3.06,Std:0.13,Min:2.7,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.080815
#P15119
Spike_AFFX-r2-Bs-phe_M_signal30.071955
Corner-Avg:7902,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal6.601691
Spike_AFFX-r2-Ec-bioB_3_signal8.910229
Spike_AFFX-r2-Bs-lys_M_signal13.096020
Spike_AFFX-r2-P1-cre_3_signal3398.017578
Spike_AFFX-r2-Bs-lys_3-5-ratio2.147747
Spike_AFFX-r2-Bs-dap_M_signal191.210739
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio14.651295
Spike_AFFX-r2-Ec-bioB_avg-signal9.116732
Spike_AFFX-r2-Bs-thr_avg-signal56.177044
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal751.499939
Spike_AFFX-r2-Bs-phe_5_signal24.074015
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1186.894287
RawQ2.662654
Spike_AFFX-r2-Bs-lys_5_signal21.186270
Signal(A)3.831381
%A32.073650
Signal(All)134.088104
Corner+Avg:144,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal197.486816
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal41.365303
Spike_AFFX-r2-Ec-bioD_avg-signal969.197144
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.282333
Spike_AFFX-r2-Bs-lys_avg-signal26.595015
Spike_AFFX-r2-P1-cre_avg-signal3287.414551
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.644016
Spike_AFFX-r2-Bs-thr_3_signal118.394409
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-signal31.837090
Spike_AFFX-r2-Bs-dap_3_signal356.192230
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.579367
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal189.197662
#M375
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal45.502754
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.043812
Spike_AFFX-r2-Bs-thr_M_signal42.055901
Signal(P)200.089279
Spike_AFFX-r2-Bs-phe_3-5-ratio1.718255
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5593,Count:9
Spike_AFFX-r2-P1-cre_5_signal3176.811768
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7316
Signal(M)14.319154
BackgroundAvg:63.36,Std:0.61,Min:61.3,Max:65.1
Spike_AFFX-r2-Ec-bioC_avg-signal193.342239
Spike_AFFX-r2-Bs-dap_avg-signal200.203995
Spike_AFFX-r2-Bs-dap_3-5-ratio6.694207
Spike_AFFX-r2-Ec-bioB_5_signal11.838276
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.479832
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-5_Col-0-mock-1h_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 ("Quint_623-5_Col-0-mock-1h_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: Quint_623-5_Col-0-mock-1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with mock (liquid ATS medium + 0.1% Ethanol) for 1 h in the dark before roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.397363
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-ratio1.128739
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.992141
Spike_AFFX-r2-Bs-dap_5_signal25.295448
NoiseAvg:3.86,Std:0.06,Min:3.7,Max:4.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal0.729331
#P15109
Spike_AFFX-r2-Bs-phe_M_signal18.265989
Corner-Avg:13584,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal6.690948
Spike_AFFX-r2-Ec-bioB_3_signal9.236704
Spike_AFFX-r2-Bs-lys_M_signal13.453900
Spike_AFFX-r2-P1-cre_3_signal3079.614746
Spike_AFFX-r2-Bs-lys_3-5-ratio2.146322
Spike_AFFX-r2-Bs-dap_M_signal119.619049
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio67.161705
Spike_AFFX-r2-Ec-bioB_avg-signal8.412508
Spike_AFFX-r2-Bs-thr_avg-signal31.548223
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal646.960449
Spike_AFFX-r2-Bs-phe_5_signal15.298272
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal906.653992
RawQ3.004334
Spike_AFFX-r2-Bs-lys_5_signal14.874984
Signal(A)4.128608
%A32.135029
Signal(All)133.957672
Corner+Avg:252,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal161.588791
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal36.646923
Spike_AFFX-r2-Ec-bioD_avg-signal776.807251
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.238495
Spike_AFFX-r2-Bs-lys_avg-signal20.085131
Spike_AFFX-r2-P1-cre_avg-signal2903.990723
Spike_AFFX-r2-Ec-bioB_M_detectionM
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.626480
Spike_AFFX-r2-Bs-thr_3_signal67.161705
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal23.403727
Spike_AFFX-r2-Bs-dap_3_signal202.829041
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.401406
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal147.415817
#M371
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal31.926508
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.096143
Spike_AFFX-r2-Bs-thr_M_signal26.753630
Signal(P)199.845886
Spike_AFFX-r2-Bs-phe_3-5-ratio2.395494
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10716,Count:9
Spike_AFFX-r2-P1-cre_5_signal2728.366699
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7330
Signal(M)15.742405
BackgroundAvg:74.34,Std:0.89,Min:71.6,Max:76.6
Spike_AFFX-r2-Ec-bioC_avg-signal154.502304
Spike_AFFX-r2-Bs-dap_avg-signal115.914513
Spike_AFFX-r2-Bs-dap_3-5-ratio8.018401
Spike_AFFX-r2-Ec-bioB_5_signal9.309872
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.397363
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-6_Col-0-mock-1h_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 ("Quint_623-6_Col-0-mock-1h_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: Quint_623-6_Col-0-mock-1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with mock (liquid ATS medium + 0.1% Ethanol) for 1 h in the dark before roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.268375
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-ratio1.161550
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.807627
Spike_AFFX-r2-Bs-dap_5_signal11.879465
NoiseAvg:4.02,Std:0.13,Min:3.7,Max:4.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionM
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.595670
#P15563
Spike_AFFX-r2-Bs-phe_M_signal11.070379
Corner-Avg:8700,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal4.785936
Spike_AFFX-r2-Ec-bioB_3_signal6.868634
Spike_AFFX-r2-Bs-lys_M_signal7.770863
Spike_AFFX-r2-P1-cre_3_signal2600.061523
Spike_AFFX-r2-Bs-lys_3-5-ratio3.169879
Spike_AFFX-r2-Bs-dap_M_signal88.049995
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.832222
Spike_AFFX-r2-Ec-bioB_avg-signal6.719761
Spike_AFFX-r2-Bs-thr_avg-signal21.502312
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal530.792114
Spike_AFFX-r2-Bs-phe_5_signal12.562915
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal763.609253
RawQ3.071664
Spike_AFFX-r2-Bs-lys_5_signal9.379333
Signal(A)2.955267
%A30.486629
Signal(All)131.634384
Corner+Avg:158,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal150.621231
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal17.951447
Spike_AFFX-r2-Ec-bioD_avg-signal647.200684
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.228844
Spike_AFFX-r2-Bs-lys_avg-signal15.627181
Spike_AFFX-r2-P1-cre_avg-signal2419.251465
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.284524
Spike_AFFX-r2-Bs-thr_3_signal38.230862
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-signal13.861580
Spike_AFFX-r2-Bs-dap_3_signal154.021515
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.438622
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal151.225815
#M293
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal29.731346
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.996002
Spike_AFFX-r2-Bs-thr_M_signal20.680401
Signal(P)191.371445
Spike_AFFX-r2-Bs-phe_3-5-ratio1.428924
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6872,Count:9
Spike_AFFX-r2-P1-cre_5_signal2238.441406
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6954
Signal(M)12.681543
BackgroundAvg:78.93,Std:1.05,Min:76.1,Max:81.2
Spike_AFFX-r2-Ec-bioC_avg-signal150.923523
Spike_AFFX-r2-Bs-dap_avg-signal84.650322
Spike_AFFX-r2-Bs-dap_3-5-ratio12.965358
Spike_AFFX-r2-Ec-bioB_5_signal8.504711
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.268375
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-7_pdr9-1-mock-1h_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 ("Quint_623-7_pdr9-1-mock-1h_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: Quint_623-7_pdr9-1-mock-1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: pdr9-1
Stock Code:
Genetic Background: Col-0
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At3g53480
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with mock (liquid ATS medium + 0.1% Ethanol) for 1 h in the dark before roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.356959
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-ratio1.183087
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.564084
Spike_AFFX-r2-Bs-dap_5_signal20.107471
NoiseAvg:3.63,Std:0.14,Min:3.3,Max:4.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionM
Spike_AFFX-r2-Bs-thr_5_signal3.741211
#P15383
Spike_AFFX-r2-Bs-phe_M_signal15.600842
Corner-Avg:9772,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal6.711106
Spike_AFFX-r2-Ec-bioB_3_signal8.245943
Spike_AFFX-r2-Bs-lys_M_signal15.271645
Spike_AFFX-r2-P1-cre_3_signal3152.358887
Spike_AFFX-r2-Bs-lys_3-5-ratio2.040552
Spike_AFFX-r2-Bs-dap_M_signal132.439743
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio22.975149
Spike_AFFX-r2-Ec-bioB_avg-signal9.858444
Spike_AFFX-r2-Bs-thr_avg-signal38.092739
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal611.657532
Spike_AFFX-r2-Bs-phe_5_signal19.039278
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal826.420898
RawQ2.906664
Spike_AFFX-r2-Bs-lys_5_signal14.157305
Signal(A)3.701785
%A30.955721
Signal(All)132.851761
Corner+Avg:179,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal177.960495
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal43.417725
Spike_AFFX-r2-Ec-bioD_avg-signal719.039185
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.439720
Spike_AFFX-r2-Bs-lys_avg-signal19.439224
Spike_AFFX-r2-P1-cre_avg-signal2908.438965
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_signal85.954872
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-signal26.019281
Spike_AFFX-r2-Bs-dap_3_signal260.279022
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.351117
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal173.125412
#M366
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.888723
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.027928
Spike_AFFX-r2-Bs-thr_M_signal24.582132
Signal(P)194.949036
Spike_AFFX-r2-Bs-phe_3-5-ratio2.280429
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7834,Count:9
Spike_AFFX-r2-P1-cre_5_signal2664.519287
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7061
Signal(M)14.506181
BackgroundAvg:70.30,Std:0.68,Min:68.4,Max:71.9
Spike_AFFX-r2-Ec-bioC_avg-signal175.542953
Spike_AFFX-r2-Bs-dap_avg-signal137.608749
Spike_AFFX-r2-Bs-dap_3-5-ratio12.944393
Spike_AFFX-r2-Ec-bioB_5_signal14.618285
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.356959
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-8_pdr9-1-mock-1h_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 ("Quint_623-8_pdr9-1-mock-1h_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: Quint_623-8_pdr9-1-mock-1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: pdr9-1
Stock Code:
Genetic Background: Col-0
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At3g53480
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with mock (liquid ATS medium + 0.1% Ethanol) for 1 h in the dark before roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.331319
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-ratio1.096107
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.516858
Spike_AFFX-r2-Bs-dap_5_signal10.210162
NoiseAvg:3.90,Std:0.13,Min:3.5,Max:4.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal4.815150
#P15283
Spike_AFFX-r2-Bs-phe_M_signal8.599957
Corner-Avg:8468,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal10.135636
Spike_AFFX-r2-Ec-bioB_3_signal6.827914
Spike_AFFX-r2-Bs-lys_M_signal6.166270
Spike_AFFX-r2-P1-cre_3_signal3057.349609
Spike_AFFX-r2-Bs-lys_3-5-ratio2.911230
Spike_AFFX-r2-Bs-dap_M_signal66.716682
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.399286
Spike_AFFX-r2-Ec-bioB_avg-signal10.057988
Spike_AFFX-r2-Bs-thr_avg-signal16.221266
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal647.099976
Spike_AFFX-r2-Bs-phe_5_signal10.032210
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal837.192383
RawQ3.140861
Spike_AFFX-r2-Bs-lys_5_signal6.472737
Signal(A)3.625454
%A31.420429
Signal(All)133.004425
Corner+Avg:161,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal193.155685
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal19.150551
Spike_AFFX-r2-Ec-bioD_avg-signal742.146179
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.001312
Spike_AFFX-r2-Bs-lys_avg-signal10.494210
Spike_AFFX-r2-P1-cre_avg-signal2923.314453
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.578255
Spike_AFFX-r2-Bs-thr_3_signal25.998369
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal12.594239
Spike_AFFX-r2-Bs-dap_3_signal148.877838
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.293761
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal158.953369
#M360
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.843626
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.215172
Spike_AFFX-r2-Bs-thr_M_signal17.850277
Signal(P)196.478149
Spike_AFFX-r2-Bs-phe_3-5-ratio1.908906
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7236,Count:9
Spike_AFFX-r2-P1-cre_5_signal2789.279541
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7167
Signal(M)14.088443
BackgroundAvg:79.92,Std:0.62,Min:78.4,Max:82.2
Spike_AFFX-r2-Ec-bioC_avg-signal176.054535
Spike_AFFX-r2-Bs-dap_avg-signal75.268227
Spike_AFFX-r2-Bs-dap_3-5-ratio14.581339
Spike_AFFX-r2-Ec-bioB_5_signal13.210413
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.331319
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-9_pdr9-1-mock-1h_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 ("Quint_623-9_pdr9-1-mock-1h_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: Quint_623-9_pdr9-1-mock-1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: pdr9-1
Stock Code:
Genetic Background: Col-0
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At3g53480
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with mock (liquid ATS medium + 0.1% Ethanol) for 1 h in the dark before roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.568386
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-ratio1.018609
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.268924
Spike_AFFX-r2-Bs-dap_5_signal28.040485
NoiseAvg:3.01,Std:0.11,Min:2.7,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal6.981276
#P15058
Spike_AFFX-r2-Bs-phe_M_signal14.424190
Corner-Avg:10714,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal4.758648
Spike_AFFX-r2-Ec-bioB_3_signal4.985970
Spike_AFFX-r2-Bs-lys_M_signal14.080595
Spike_AFFX-r2-P1-cre_3_signal3446.192383
Spike_AFFX-r2-Bs-lys_3-5-ratio2.126394
Spike_AFFX-r2-Bs-dap_M_signal99.904106
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.949060
Spike_AFFX-r2-Ec-bioB_avg-signal9.428358
Spike_AFFX-r2-Bs-thr_avg-signal25.764145
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal590.970886
Spike_AFFX-r2-Bs-phe_5_signal16.551208
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal908.378113
RawQ2.574366
Spike_AFFX-r2-Bs-lys_5_signal16.260868
Signal(A)4.611088
%A32.262165
Signal(All)135.891739
Corner+Avg:175,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal173.271591
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal40.111980
Spike_AFFX-r2-Ec-bioD_avg-signal749.674500
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.014908
Spike_AFFX-r2-Bs-lys_avg-signal21.639490
Spike_AFFX-r2-P1-cre_avg-signal3414.712402
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.722929
Spike_AFFX-r2-Bs-thr_3_signal48.513306
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal23.695793
Spike_AFFX-r2-Bs-dap_3_signal236.515457
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.537094
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal152.115173
#M393
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal34.577011
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.139082
Spike_AFFX-r2-Bs-thr_M_signal21.797848
Signal(P)203.181396
Spike_AFFX-r2-Bs-phe_3-5-ratio2.423508
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9356,Count:9
Spike_AFFX-r2-P1-cre_5_signal3383.232666
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7359
Signal(M)15.908479
BackgroundAvg:62.11,Std:0.88,Min:60.5,Max:64.3
Spike_AFFX-r2-Ec-bioC_avg-signal162.693390
Spike_AFFX-r2-Bs-dap_avg-signal121.486687
Spike_AFFX-r2-Bs-dap_3-5-ratio8.434785
Spike_AFFX-r2-Ec-bioB_5_signal18.540457
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.568386
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-10_pdr9-2-IPA[5µM]-1h_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 ("Quint_623-10_pdr9-2-IPA[5µM]-1h_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: Quint_623-10_pdr9-2-IPA[5µM]-1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_050885 (L) (N) (homozygous)
Stock Code: CS859461
Genetic Background: Col-0 (Columbia, N60000)
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA Insertion
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with idole-3-propionic acid (liquid ATS medium + 5 µM indole-3-propionic acid in 0.1% Ethanol) for 1 h in the dark before roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.445813
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-ratio1.063266
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.365381
Spike_AFFX-r2-Bs-dap_5_signal18.854046
NoiseAvg:3.16,Std:0.13,Min:2.8,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.600854
#P15391
Spike_AFFX-r2-Bs-phe_M_signal13.203050
Corner-Avg:7460,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal5.902454
Spike_AFFX-r2-Ec-bioB_3_signal9.830593
Spike_AFFX-r2-Bs-lys_M_signal10.919688
Spike_AFFX-r2-P1-cre_3_signal3145.677490
Spike_AFFX-r2-Bs-lys_3-5-ratio3.270846
Spike_AFFX-r2-Bs-dap_M_signal88.070534
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.786845
Spike_AFFX-r2-Ec-bioB_avg-signal7.644313
Spike_AFFX-r2-Bs-thr_avg-signal25.958330
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal620.912842
Spike_AFFX-r2-Bs-phe_5_signal23.778082
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal919.821472
RawQ2.647182
Spike_AFFX-r2-Bs-lys_5_signal8.740407
Signal(A)3.244821
%A31.109163
Signal(All)133.625320
Corner+Avg:134,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal177.391708
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal24.333241
Spike_AFFX-r2-Ec-bioD_avg-signal770.367188
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.474792
Spike_AFFX-r2-Bs-lys_avg-signal16.082872
Spike_AFFX-r2-P1-cre_avg-signal3052.091797
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.416046
Spike_AFFX-r2-Bs-thr_3_signal54.814690
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal20.438124
Spike_AFFX-r2-Bs-dap_3_signal176.090073
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.481402
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal172.130127
#M323
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.588524
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.030567
Spike_AFFX-r2-Bs-thr_M_signal17.459454
Signal(P)196.278961
Spike_AFFX-r2-Bs-phe_3-5-ratio1.023347
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6071,Count:9
Spike_AFFX-r2-P1-cre_5_signal2958.506104
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7096
Signal(M)12.503881
BackgroundAvg:66.84,Std:0.37,Min:66.0,Max:68.2
Spike_AFFX-r2-Ec-bioC_avg-signal174.760925
Spike_AFFX-r2-Bs-dap_avg-signal94.338219
Spike_AFFX-r2-Bs-dap_3-5-ratio9.339643
Spike_AFFX-r2-Ec-bioB_5_signal7.199893
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.445813
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-11_pdr9-2-IPA[5µM]-1h_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 ("Quint_623-11_pdr9-2-IPA[5µM]-1h_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: Quint_623-11_pdr9-2-IPA[5µM]-1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_050885 (L) (N) (homozygous)
Stock Code: CS859461
Genetic Background: Col-0 (Columbia, N60000)
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA Insertion
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with idole-3-propionic acid (liquid ATS medium + 5 µM indole-3-propionic acid in 0.1% Ethanol) for 1 h in the dark before roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.433242
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-ratio1.102848
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.537104
Spike_AFFX-r2-Bs-dap_5_signal20.481075
NoiseAvg:3.35,Std:0.08,Min:3.1,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal7.267615
#P15299
Spike_AFFX-r2-Bs-phe_M_signal10.131835
Corner-Avg:7721,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal5.332790
Spike_AFFX-r2-Ec-bioB_3_signal4.102951
Spike_AFFX-r2-Bs-lys_M_signal16.628204
Spike_AFFX-r2-P1-cre_3_signal3061.090576
Spike_AFFX-r2-Bs-lys_3-5-ratio1.869696
Spike_AFFX-r2-Bs-dap_M_signal80.092804
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.624268
Spike_AFFX-r2-Ec-bioB_avg-signal5.691587
Spike_AFFX-r2-Bs-thr_avg-signal22.950478
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal560.326538
Spike_AFFX-r2-Bs-phe_5_signal15.278363
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal802.844177
RawQ2.783735
Spike_AFFX-r2-Bs-lys_5_signal12.422488
Signal(A)3.859733
%A31.398510
Signal(All)134.193451
Corner+Avg:136,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal167.154480
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal24.465025
Spike_AFFX-r2-Ec-bioD_avg-signal681.585327
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.071457
Spike_AFFX-r2-Bs-lys_avg-signal17.425657
Spike_AFFX-r2-P1-cre_avg-signal2918.356445
Spike_AFFX-r2-Ec-bioB_M_detectionM
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.530031
Spike_AFFX-r2-Bs-thr_3_signal40.875015
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-signal16.625074
Spike_AFFX-r2-Bs-dap_3_signal190.374649
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.432815
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal153.020340
#M349
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal23.226280
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.092368
Spike_AFFX-r2-Bs-thr_M_signal20.708803
Signal(P)197.932388
Spike_AFFX-r2-Bs-phe_3-5-ratio1.601286
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6596,Count:9
Spike_AFFX-r2-P1-cre_5_signal2775.622559
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7162
Signal(M)14.733066
BackgroundAvg:70.47,Std:0.66,Min:68.7,Max:71.8
Spike_AFFX-r2-Ec-bioC_avg-signal160.087402
Spike_AFFX-r2-Bs-dap_avg-signal96.982849
Spike_AFFX-r2-Bs-dap_3-5-ratio9.295149
Spike_AFFX-r2-Ec-bioB_5_signal7.639018
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.433242
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-12_pdr9-2-IPA[5µM]-1h_Rep3_ATH1

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

Summary Information

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

  • Extract 1 ("Quint_623-12_pdr9-2-IPA[5µM]-1h_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: Quint_623-12_pdr9-2-IPA[5µM]-1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_050885 (L) (N) (homozygous)
Stock Code: CS859461
Genetic Background: Col-0 (Columbia, N60000)
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA Insertion
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with idole-3-propionic acid (liquid ATS medium + 5 µM indole-3-propionic acid in 0.1% Ethanol) for 1 h in the dark before roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.51459
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-ratio1.039063
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.255868
Spike_AFFX-r2-Bs-dap_5_signal20.768883
NoiseAvg:3.19,Std:0.12,Min:3.0,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal3.851420
#P15028
Spike_AFFX-r2-Bs-phe_M_signal14.728883
Corner-Avg:7514,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal8.374656
Spike_AFFX-r2-Ec-bioB_3_signal10.830292
Spike_AFFX-r2-Bs-lys_M_signal14.374010
Spike_AFFX-r2-P1-cre_3_signal3084.861328
Spike_AFFX-r2-Bs-lys_3-5-ratio1.778091
Spike_AFFX-r2-Bs-dap_M_signal90.329422
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio13.360643
Spike_AFFX-r2-Ec-bioB_avg-signal9.276233
Spike_AFFX-r2-Bs-thr_avg-signal26.194475
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal555.088623
Spike_AFFX-r2-Bs-phe_5_signal15.742034
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal863.836731
RawQ2.672017
Spike_AFFX-r2-Bs-lys_5_signal13.828481
Signal(A)4.260214
%A32.547127
Signal(All)134.708191
Corner+Avg:130,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal191.877731
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal27.395327
Spike_AFFX-r2-Ec-bioD_avg-signal709.462646
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.883385
Spike_AFFX-r2-Bs-lys_avg-signal17.596928
Spike_AFFX-r2-P1-cre_avg-signal3026.875000
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.569487
Spike_AFFX-r2-Bs-thr_3_signal51.457447
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-signal19.288748
Spike_AFFX-r2-Bs-dap_3_signal191.725082
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.556214
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal163.373550
#M358
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.588293
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.174472
Spike_AFFX-r2-Bs-thr_M_signal23.274565
Signal(P)201.989624
Spike_AFFX-r2-Bs-phe_3-5-ratio1.740266
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6423,Count:9
Spike_AFFX-r2-P1-cre_5_signal2968.888916
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7424
Signal(M)15.547865
BackgroundAvg:68.12,Std:0.46,Min:66.5,Max:70.0
Spike_AFFX-r2-Ec-bioC_avg-signal177.625641
Spike_AFFX-r2-Bs-dap_avg-signal100.941132
Spike_AFFX-r2-Bs-dap_3-5-ratio9.231362
Spike_AFFX-r2-Ec-bioB_5_signal8.623748
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.514590
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-13_Col-0-IPA[5µM]-1h_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 ("Quint_623-13_Col-0-IPA[5µM]-1h_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: Quint_623-13_Col-0-IPA[5µM]-1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with idole-3-propionic acid (liquid ATS medium + 5 µM indole-3-propionic acid in 0.1% Ethanol) for 1 h in the dark before roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.419396
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-ratio1.286868
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.759493
Spike_AFFX-r2-Bs-dap_5_signal24.066647
NoiseAvg:3.08,Std:0.08,Min:2.9,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.918073
#P15307
Spike_AFFX-r2-Bs-phe_M_signal12.262568
Corner-Avg:8077,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal8.774681
Spike_AFFX-r2-Ec-bioB_3_signal6.721729
Spike_AFFX-r2-Bs-lys_M_signal10.283629
Spike_AFFX-r2-P1-cre_3_signal3368.648926
Spike_AFFX-r2-Bs-lys_3-5-ratio1.621736
Spike_AFFX-r2-Bs-dap_M_signal108.206924
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.441929
Spike_AFFX-r2-Ec-bioB_avg-signal8.115564
Spike_AFFX-r2-Bs-thr_avg-signal25.202660
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal559.479248
Spike_AFFX-r2-Bs-phe_5_signal16.270491
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal782.748779
RawQ2.594248
Spike_AFFX-r2-Bs-lys_5_signal16.436003
Signal(A)3.837063
%A31.008329
Signal(All)133.722122
Corner+Avg:144,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal172.499481
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal32.959019
Spike_AFFX-r2-Ec-bioD_avg-signal671.114014
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.106529
Spike_AFFX-r2-Bs-lys_avg-signal17.791498
Spike_AFFX-r2-P1-cre_avg-signal2993.180176
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.885138
Spike_AFFX-r2-Bs-thr_3_signal44.041882
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal20.497360
Spike_AFFX-r2-Bs-dap_3_signal220.975174
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.399067
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal147.276520
#M430
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.654863
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.171263
Spike_AFFX-r2-Bs-thr_M_signal25.648024
Signal(P)197.104355
Spike_AFFX-r2-Bs-phe_3-5-ratio2.025693
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6149,Count:9
Spike_AFFX-r2-P1-cre_5_signal2617.711426
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7073
Signal(M)13.920516
BackgroundAvg:57.03,Std:0.29,Min:56.0,Max:58.1
Spike_AFFX-r2-Ec-bioC_avg-signal159.888000
Spike_AFFX-r2-Bs-dap_avg-signal117.749580
Spike_AFFX-r2-Bs-dap_3-5-ratio9.181802
Spike_AFFX-r2-Ec-bioB_5_signal8.850283
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.419396
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-14_Col-0-IPA[5µM]-1h_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 ("Quint_623-14_Col-0-IPA[5µM]-1h_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: Quint_623-14_Col-0-IPA[5µM]-1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with idole-3-propionic acid (liquid ATS medium + 5 µM indole-3-propionic acid in 0.1% Ethanol) for 1 h in the dark before roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.385239
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-ratio1.109970
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.432831
Spike_AFFX-r2-Bs-dap_5_signal22.915155
NoiseAvg:3.21,Std:0.07,Min:3.0,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal2.700022
#P15361
Spike_AFFX-r2-Bs-phe_M_signal17.131653
Corner-Avg:11076,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal7.582123
Spike_AFFX-r2-Ec-bioB_3_signal10.047812
Spike_AFFX-r2-Bs-lys_M_signal13.398847
Spike_AFFX-r2-P1-cre_3_signal3584.396484
Spike_AFFX-r2-Bs-lys_3-5-ratio2.246342
Spike_AFFX-r2-Bs-dap_M_signal103.114052
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio17.684116
Spike_AFFX-r2-Ec-bioB_avg-signal8.214166
Spike_AFFX-r2-Bs-thr_avg-signal23.585810
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal780.913818
Spike_AFFX-r2-Bs-phe_5_signal20.634861
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1033.164185
RawQ2.784062
Spike_AFFX-r2-Bs-lys_5_signal13.720567
Signal(A)3.339268
%A31.056555
Signal(All)135.653748
Corner+Avg:206,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal193.086639
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal30.402029
Spike_AFFX-r2-Ec-bioD_avg-signal907.039001
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.343269
Spike_AFFX-r2-Bs-lys_avg-signal19.313499
Spike_AFFX-r2-P1-cre_avg-signal3406.835205
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_signal47.747513
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal22.722849
Spike_AFFX-r2-Bs-dap_3_signal217.128403
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.323020
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal183.734756
#M365
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal30.821087
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.050899
Spike_AFFX-r2-Bs-thr_M_signal20.309900
Signal(P)199.574753
Spike_AFFX-r2-Bs-phe_3-5-ratio1.473333
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8846,Count:9
Spike_AFFX-r2-P1-cre_5_signal3229.273926
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7084
Signal(M)13.531200
BackgroundAvg:68.67,Std:0.49,Min:67.6,Max:70.6
Spike_AFFX-r2-Ec-bioC_avg-signal188.410706
Spike_AFFX-r2-Bs-dap_avg-signal114.385872
Spike_AFFX-r2-Bs-dap_3-5-ratio9.475319
Spike_AFFX-r2-Ec-bioB_5_signal7.012559
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.385239
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-15_Col-0-IPA[5µM]-1h_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 ("Quint_623-15_Col-0-IPA[5µM]-1h_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: Quint_623-15_Col-0-IPA[5µM]-1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with idole-3-propionic acid (liquid ATS medium + 5 µM indole-3-propionic acid in 0.1% Ethanol) for 1 h in the dark before roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.476346
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.950169
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.566689
Spike_AFFX-r2-Bs-dap_5_signal7.054923
NoiseAvg:3.17,Std:0.11,Min:2.8,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionM
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal2.122447
#P15133
Spike_AFFX-r2-Bs-phe_M_signal8.774900
Corner-Avg:7211,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal10.307336
Spike_AFFX-r2-Ec-bioB_3_signal6.046204
Spike_AFFX-r2-Bs-lys_M_signal7.047130
Spike_AFFX-r2-P1-cre_3_signal2705.601074
Spike_AFFX-r2-Bs-lys_3-5-ratio1.932114
Spike_AFFX-r2-Bs-dap_M_signal65.190475
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio16.725002
Spike_AFFX-r2-Ec-bioB_avg-signal9.007630
Spike_AFFX-r2-Bs-thr_avg-signal17.386301
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal585.256226
Spike_AFFX-r2-Bs-phe_5_signal14.369118
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal937.787048
RawQ2.806427
Spike_AFFX-r2-Bs-lys_5_signal10.614333
Signal(A)3.683574
%A32.051731
Signal(All)136.552460
Corner+Avg:142,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal162.163971
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal30.477348
Spike_AFFX-r2-Ec-bioD_avg-signal761.521606
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.343712
Spike_AFFX-r2-Bs-lys_avg-signal12.723187
Spike_AFFX-r2-P1-cre_avg-signal2776.547852
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.604559
Spike_AFFX-r2-Bs-thr_3_signal35.497940
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal17.873789
Spike_AFFX-r2-Bs-dap_3_signal140.233963
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.602353
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal154.817978
#M366
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal20.508099
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.047449
Spike_AFFX-r2-Bs-thr_M_signal14.538518
Signal(P)203.672440
Spike_AFFX-r2-Bs-phe_3-5-ratio2.121031
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5380,Count:9
Spike_AFFX-r2-P1-cre_5_signal2847.494385
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7311
Signal(M)15.453292
BackgroundAvg:67.04,Std:0.69,Min:65.6,Max:69.1
Spike_AFFX-r2-Ec-bioC_avg-signal158.490967
Spike_AFFX-r2-Bs-dap_avg-signal70.826454
Spike_AFFX-r2-Bs-dap_3-5-ratio19.877462
Spike_AFFX-r2-Ec-bioB_5_signal10.669354
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.476346
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-16_pdr9-1-IPA[5µM]-1h_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 ("Quint_623-16_pdr9-1-IPA[5µM]-1h_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: Quint_623-16_pdr9-1-IPA[5µM]-1h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: pdr9-1
Stock Code:
Genetic Background: Col-0
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At3g53480
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with idole-3-propionic acid (liquid ATS medium + 5 µM indole-3-propionic acid in 0.1% Ethanol) for 1 h in the dark before roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.559592
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-ratio1.190844
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.561492
Spike_AFFX-r2-Bs-dap_5_signal22.475979
NoiseAvg:3.04,Std:0.07,Min:2.8,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal3.639863
#P14896
Spike_AFFX-r2-Bs-phe_M_signal7.559372
Corner-Avg:8000,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal12.792908
Spike_AFFX-r2-Ec-bioB_3_signal9.648796
Spike_AFFX-r2-Bs-lys_M_signal10.374167
Spike_AFFX-r2-P1-cre_3_signal3840.932129
Spike_AFFX-r2-Bs-lys_3-5-ratio2.365911
Spike_AFFX-r2-Bs-dap_M_signal74.926376
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio13.194789
Spike_AFFX-r2-Ec-bioB_avg-signal13.208633
Spike_AFFX-r2-Bs-thr_avg-signal23.588621
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal669.325562
Spike_AFFX-r2-Bs-phe_5_signal11.679615
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal925.714478
RawQ2.685847
Spike_AFFX-r2-Bs-lys_5_signal10.396259
Signal(A)4.857687
%A32.989918
Signal(All)137.804642
Corner+Avg:131,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal217.590317
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.797016
Spike_AFFX-r2-Ec-bioD_avg-signal797.520020
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.304688
Spike_AFFX-r2-Bs-lys_avg-signal15.122350
Spike_AFFX-r2-P1-cre_avg-signal3533.159180
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.705392
Spike_AFFX-r2-Bs-thr_3_signal48.027225
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-signal14.012001
Spike_AFFX-r2-Bs-dap_3_signal177.132385
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.383056
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal175.812790
#M389
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.596624
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.237625
Spike_AFFX-r2-Bs-thr_M_signal19.098776
Signal(P)208.100037
Spike_AFFX-r2-Bs-phe_3-5-ratio1.951864
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7173,Count:9
Spike_AFFX-r2-P1-cre_5_signal3225.386230
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7525
Signal(M)17.767174
BackgroundAvg:66.78,Std:0.48,Min:65.7,Max:68.5
Spike_AFFX-r2-Ec-bioC_avg-signal196.701553
Spike_AFFX-r2-Bs-dap_avg-signal91.511574
Spike_AFFX-r2-Bs-dap_3-5-ratio7.880964
Spike_AFFX-r2-Ec-bioB_5_signal17.184198
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.559592
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-17_pdr9-1-IPA[5µM]-1h_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 ("Quint_623-17_pdr9-1-IPA[5µM]-1h_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: Quint_623-17_pdr9-1-IPA[5µM]-1h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: pdr9-1
Stock Code:
Genetic Background: Col-0
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At3g53480
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with idole-3-propionic acid (liquid ATS medium + 5 µM indole-3-propionic acid in 0.1% Ethanol) for 1 h in the dark before roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.495742
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-ratio1.160076
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.207334
Spike_AFFX-r2-Bs-dap_5_signal18.694754
NoiseAvg:2.69,Std:0.06,Min:2.5,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.260020
#P15368
Spike_AFFX-r2-Bs-phe_M_signal10.136769
Corner-Avg:7806,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal12.182590
Spike_AFFX-r2-Ec-bioB_3_signal13.702368
Spike_AFFX-r2-Bs-lys_M_signal9.563753
Spike_AFFX-r2-P1-cre_3_signal4320.852539
Spike_AFFX-r2-Bs-lys_3-5-ratio1.867575
Spike_AFFX-r2-Bs-dap_M_signal93.560410
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.701558
Spike_AFFX-r2-Ec-bioB_avg-signal12.411410
Spike_AFFX-r2-Bs-thr_avg-signal22.719976
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal897.572998
Spike_AFFX-r2-Bs-phe_5_signal23.385658
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1180.231689
RawQ2.533164
Spike_AFFX-r2-Bs-lys_5_signal13.044032
Signal(A)3.231379
%A31.201227
Signal(All)136.612595
Corner+Avg:129,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal228.938629
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal29.404955
Spike_AFFX-r2-Ec-bioD_avg-signal1038.902344
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.373962
Spike_AFFX-r2-Bs-lys_avg-signal15.656165
Spike_AFFX-r2-P1-cre_avg-signal4022.740967
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.424814
Spike_AFFX-r2-Bs-thr_3_signal45.770370
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal20.975794
Spike_AFFX-r2-Bs-dap_3_signal203.510727
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.314914
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal216.556366
#M325
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.360710
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.057178
Spike_AFFX-r2-Bs-thr_M_signal17.129538
Signal(P)200.982437
Spike_AFFX-r2-Bs-phe_3-5-ratio1.257393
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6208,Count:9
Spike_AFFX-r2-P1-cre_5_signal3724.629395
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7117
Signal(M)13.653658
BackgroundAvg:59.70,Std:0.64,Min:58.2,Max:61.4
Spike_AFFX-r2-Ec-bioC_avg-signal222.747498
Spike_AFFX-r2-Bs-dap_avg-signal105.255302
Spike_AFFX-r2-Bs-dap_3-5-ratio10.885981
Spike_AFFX-r2-Ec-bioB_5_signal11.349274
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.495742
NF1.000000
HZ4
Tau0.015000

Slide: Quint_623-18_pdr9-1-IPA[5µM]-1h_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 ("Quint_623-18_pdr9-1-IPA[5µM]-1h_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: Quint_623-18_pdr9-1-IPA[5µM]-1h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: pdr9-1
Stock Code:
Genetic Background: Col-0
Age: 7 d
Growth Conditions:
Stratificationseeds were stratified in sterile, deionized water for 4d in the dark at 4°C after surface sterilization
Sterilisationseeds were incubated on a shaker for 3 min in 70 % Ethanol, 10 min in bleach followed by washing 5 times with sterilized dH2O.
ProtocolAfter stratification, seedlings were germinated and grown under sterile, long day (16/8 light/dark) conditions on vertical ATS nutrient medium plates (Lincoln et al., 1990).
Percentage Agrose1.5 % (agargel)
Substrate Sterilising Procedureautoclaving
Temperature22 °C average, 22 °C day, 22 °C night
Humidity40 % average, 40 % day, 40 % night
MediumOwn medium: Arabidopsis thaliana solution (ATS) nutrient medium (Lincoln et al., 1990).
Lighting(Source: Cool white fluorescent. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: EMS induced mutation mutation in At3g53480
Tissue: roots
in vivo Treatment: 7 d old seedlings grown on vertical plates were treated with idole-3-propionic acid (liquid ATS medium + 5 µM indole-3-propionic acid in 0.1% Ethanol) for 1 h in the dark before roots were harvested and frozen in liquid nitrogen.
Additional Organism Information:
Sample Description7 d old seedlings
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:0.521179
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.938721
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.237488
Spike_AFFX-r2-Bs-dap_5_signal14.563679
NoiseAvg:2.75,Std:0.26,Min:2.0,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal1.482429
#P14885
Spike_AFFX-r2-Bs-phe_M_signal9.416773
Corner-Avg:239,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal7.949472
Spike_AFFX-r2-Ec-bioB_3_signal7.268302
Spike_AFFX-r2-Bs-lys_M_signal15.495247
Spike_AFFX-r2-P1-cre_3_signal2915.357178
Spike_AFFX-r2-Bs-lys_3-5-ratio1.594332
Spike_AFFX-r2-Bs-dap_M_signal106.170082
Spike_AFFX-r2-Bs-thr_M_detectionM
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio32.099270
Spike_AFFX-r2-Ec-bioB_avg-signal7.030403
Spike_AFFX-r2-Bs-thr_avg-signal22.401190
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal550.217590
Spike_AFFX-r2-Bs-phe_5_signal14.378580
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal868.929443
RawQ2.533466
Spike_AFFX-r2-Bs-lys_5_signal10.486777
Signal(A)4.058196
%A32.854012
Signal(All)135.436035
Corner+Avg:16,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal176.243484
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal34.803001
Spike_AFFX-r2-Ec-bioD_avg-signal709.573486
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionM
%P65.256470
Spike_AFFX-r2-Bs-lys_avg-signal14.233811
Spike_AFFX-r2-P1-cre_avg-signal3010.513184
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.889522
Spike_AFFX-r2-Bs-thr_3_signal47.584900
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-signal19.532784
Spike_AFFX-r2-Bs-dap_3_signal168.877930
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.579247
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal154.963211
#M431
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal16.719410
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.137325
Spike_AFFX-r2-Bs-thr_M_signal18.136236
Signal(P)205.063248
Spike_AFFX-r2-Bs-phe_3-5-ratio2.420475
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7576,Count:9
Spike_AFFX-r2-P1-cre_5_signal3105.668945
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7494
Signal(M)15.121659
BackgroundAvg:58.56,Std:2.21,Min:53.6,Max:62.8
Spike_AFFX-r2-Ec-bioC_avg-signal165.603348
Spike_AFFX-r2-Bs-dap_avg-signal96.537231
Spike_AFFX-r2-Bs-dap_3-5-ratio11.595829
Spike_AFFX-r2-Ec-bioB_5_signal5.873432
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.521179
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team