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Experiment: Microarray Analysis of cpl3 Mutant

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-657

An Arabidopsis (Arabidopsis thaliana) multigene family (predicted to be more than 20 members) encodes plant C-terminal domain (CTD) phosphatases that dephosphorylate Ser residues in tandem heptad repeat sequences of the RNA polymerase II C terminus. CTD phosphatase-like (CPL) isoform 3 (CPL3)is a regulator of osmotic stress and abscisic acid (ABA) signaling. Recombinant CPL3 interacts with AtRAP74, an Arabidopsis ortholog of a FCP1-interacting TFIIF subunit. A CPL3 C-terminal fragment that contains the BRCT domain mediates molecular interaction with AtRAP74. Consistent with its predicted role in transcriptional regulation, green fluorescent protein fusion protein of CPL3 co-localizes to the nucleus with AtRAP74. cpl3 mutations that eliminate the BRCT or FCP1 homology domain cause ABA hyperactivation of the stress-inducible RD29a promoter. Hence, CPL3 is an isoform that specially facilitates ABA signaling.Reference:Bang et.al., 2006.

About the Experimenter

Name: Hisashi koiwa
Head of Lab Name: Hisashi koiwa
Lab:
Address:Department of Horticultural Sciences, College of Agriculture and Life Science, Texas A
&
M University
202 Horticulture/Forest Science Building, , College Station, Texas, TX 77843-2133, UNITED STATES
Postcode: TX 77843-2133
Country: UNITED STATES
 
Telephone Number: +1 979-845-5282
Fax Number: +1 979-845-0627

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:6
 
Experimental Parameters:
parametergenetic_modification
Quality Control Measures Taken:
References:
Reference Bang et.al., 2006.
 
Other Information:

Slides in this Experiment

Hybridisation Set: koiwa: Microarray Analysis of cpl3 Mutant

Slide: koiwa_657-1_C24_WT_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("koiwa_657-1_C24_WT_Rep1_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: koiwa_657-1_C24_WT_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code: CS906
Growth Conditions:
StratificationSeeds were kept for 2 days at 4 celcius.
Sterilisation20 seconds in 70% Ethanol, then washed with sterile distilled water for three times. Then, seeds were suspended in 0.1% agar solution.
ProtocolThe seeds grown vertically for 10 days on media containing 1/4 Murashige and Skoog (MS) salts, 0.5 % sucrose, and 1.5% agar.
Plant Spacing50
Temperature25 °C average, 25 °C day, 25 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
Additional Organism Information:
Sample DescriptionWhole plant is used for sampling.
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:0.5949
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-ratio1.235541
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.232339
Spike_AFFX-r2-Bs-dap_5_signal66.042053
NoiseAvg:3.69,Std:0.15,Min:3.1,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_signal23.191902
#P14516
Spike_AFFX-r2-Bs-phe_M_signal35.491787
Corner-Avg:11037,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal91.261620
Spike_AFFX-r2-Ec-bioB_3_signal74.441429
Spike_AFFX-r2-Bs-lys_M_signal17.429380
Spike_AFFX-r2-P1-cre_3_signal4220.271484
Spike_AFFX-r2-Bs-lys_3-5-ratio1.148335
Spike_AFFX-r2-Bs-dap_M_signal262.624420
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.295125
Spike_AFFX-r2-Ec-bioB_avg-signal75.369888
Spike_AFFX-r2-Bs-thr_avg-signal75.314789
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal776.698181
Spike_AFFX-r2-Bs-phe_5_signal20.120134
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1165.915771
RawQ3.143171
Spike_AFFX-r2-Bs-lys_5_signal24.787493
Signal(A)5.900450
%A34.362122
Signal(All)139.012604
Corner+Avg:415,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal271.793335
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal57.417446
Spike_AFFX-r2-Ec-bioD_avg-signal971.307007
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.638756
Spike_AFFX-r2-Bs-lys_avg-signal23.560404
Spike_AFFX-r2-P1-cre_avg-signal3817.999023
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.999123
Spike_AFFX-r2-Bs-thr_3_signal122.804008
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-signal37.676456
Spike_AFFX-r2-Bs-dap_3_signal398.573517
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.501118
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal245.218674
#M456
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal28.464344
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.108371
Spike_AFFX-r2-Bs-thr_M_signal79.948463
Signal(P)214.632523
Spike_AFFX-r2-Bs-phe_3-5-ratio2.853731
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10459,Count:9
Spike_AFFX-r2-P1-cre_5_signal3415.726318
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7838
Signal(M)19.789165
BackgroundAvg:76.61,Std:0.84,Min:74.6,Max:78.8
Spike_AFFX-r2-Ec-bioC_avg-signal258.506012
Spike_AFFX-r2-Bs-dap_avg-signal242.413330
Spike_AFFX-r2-Bs-dap_3-5-ratio6.035147
Spike_AFFX-r2-Ec-bioB_5_signal60.406616
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.594900
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_657-2_C24_WT_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("koiwa_657-2_C24_WT_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: koiwa_657-2_C24_WT_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code: CS906
Growth Conditions:
StratificationSeeds were kept for 2 days at 4 celcius.
Sterilisation20 seconds in 70% Ethanol, then washed with sterile distilled water for three times. Then, seeds were suspended in 0.1% agar solution.
ProtocolThe seeds grown vertically for 10 days on media containing 1/4 Murashige and Skoog (MS) salts, 0.5 % sucrose, and 1.5% agar.
Plant Spacing50
Temperature25 °C average, 25 °C day, 25 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
Additional Organism Information:
Sample DescriptionWhole plant is used for sampling.
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:0.711267
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-ratio1.269440
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.470054
Spike_AFFX-r2-Bs-dap_5_signal68.018219
NoiseAvg:3.75,Std:0.11,Min:3.6,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_signal21.097057
#P13814
Spike_AFFX-r2-Bs-phe_M_signal31.143888
Corner-Avg:11316,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal104.188362
Spike_AFFX-r2-Ec-bioB_3_signal85.561722
Spike_AFFX-r2-Bs-lys_M_signal18.704283
Spike_AFFX-r2-P1-cre_3_signal4942.260254
Spike_AFFX-r2-Bs-lys_3-5-ratio3.304254
Spike_AFFX-r2-Bs-dap_M_signal185.490112
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.983008
Spike_AFFX-r2-Ec-bioB_avg-signal82.651070
Spike_AFFX-r2-Bs-thr_avg-signal68.116898
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal956.303955
Spike_AFFX-r2-Bs-phe_5_signal12.361864
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1394.835449
RawQ3.154338
Spike_AFFX-r2-Bs-lys_5_signal14.031920
Signal(A)7.440239
%A37.268742
Signal(All)145.553009
Corner+Avg:425,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal325.977203
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal40.046635
Spike_AFFX-r2-Ec-bioD_avg-signal1175.569702
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.561157
Spike_AFFX-r2-Bs-lys_avg-signal26.367079
Spike_AFFX-r2-P1-cre_avg-signal4417.759766
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.170101
Spike_AFFX-r2-Bs-thr_3_signal105.126816
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-signal27.850794
Spike_AFFX-r2-Bs-dap_3_signal333.046722
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.458569
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal307.636444
#M495
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal46.365032
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.059618
Spike_AFFX-r2-Bs-thr_M_signal78.126808
Signal(P)234.829224
Spike_AFFX-r2-Bs-phe_3-5-ratio3.239530
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10337,Count:9
Spike_AFFX-r2-P1-cre_5_signal3893.259521
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8501
Signal(M)26.027676
BackgroundAvg:78.89,Std:0.97,Min:76.8,Max:81.8
Spike_AFFX-r2-Ec-bioC_avg-signal316.806824
Spike_AFFX-r2-Bs-dap_avg-signal195.518356
Spike_AFFX-r2-Bs-dap_3-5-ratio4.896434
Spike_AFFX-r2-Ec-bioB_5_signal58.203114
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.711267
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_657-3_C24_WT_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 ("koiwa_657-3_C24_WT_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: koiwa_657-3_C24_WT_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: C24
Stock Code: CS906
Growth Conditions:
StratificationSeeds were kept for 2 days at 4 celcius.
Sterilisation20 seconds in 70% Ethanol, then washed with sterile distilled water for three times. Then, seeds were suspended in 0.1% agar solution.
ProtocolThe seeds grown vertically for 10 days on media containing 1/4 Murashige and Skoog (MS) salts, 0.5 % sucrose, and 1.5% agar.
Plant Spacing50
Temperature25 °C average, 25 °C day, 25 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
Additional Organism Information:
Sample DescriptionWhole plant is used for sampling.
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:0.574573
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-ratio1.272238
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.117618
Spike_AFFX-r2-Bs-dap_5_signal123.427795
NoiseAvg:3.59,Std:0.16,Min:3.4,Max:4.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal48.382858
#P14312
Spike_AFFX-r2-Bs-phe_M_signal67.558899
Corner-Avg:12256,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal96.990501
Spike_AFFX-r2-Ec-bioB_3_signal78.178574
Spike_AFFX-r2-Bs-lys_M_signal31.956263
Spike_AFFX-r2-P1-cre_3_signal4577.177246
Spike_AFFX-r2-Bs-lys_3-5-ratio1.533027
Spike_AFFX-r2-Bs-dap_M_signal436.810852
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.568570
Spike_AFFX-r2-Ec-bioB_avg-signal81.706703
Spike_AFFX-r2-Bs-thr_avg-signal148.324158
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal916.016052
Spike_AFFX-r2-Bs-phe_5_signal43.397926
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1458.462402
RawQ3.002784
Spike_AFFX-r2-Bs-lys_5_signal45.124439
Signal(A)5.424089
%A35.418674
Signal(All)143.740509
Corner+Avg:478,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal270.216827
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal86.195526
Spike_AFFX-r2-Ec-bioD_avg-signal1187.239258
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.744411
Spike_AFFX-r2-Bs-lys_avg-signal48.752563
Spike_AFFX-r2-P1-cre_avg-signal4087.457520
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.836914
Spike_AFFX-r2-Bs-thr_3_signal269.423309
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-signal65.717445
Spike_AFFX-r2-Bs-dap_3_signal667.498718
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.592180
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal251.773590
#M419
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal69.176987
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.073253
Spike_AFFX-r2-Bs-thr_M_signal127.166290
Signal(P)225.412354
Spike_AFFX-r2-Bs-phe_3-5-ratio1.986167
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10503,Count:9
Spike_AFFX-r2-P1-cre_5_signal3597.737793
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8079
Signal(M)20.998079
BackgroundAvg:76.85,Std:0.79,Min:75.4,Max:79.4
Spike_AFFX-r2-Ec-bioC_avg-signal260.995209
Spike_AFFX-r2-Bs-dap_avg-signal409.245758
Spike_AFFX-r2-Bs-dap_3-5-ratio5.408010
Spike_AFFX-r2-Ec-bioB_5_signal69.951057
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.574573
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_657-4_cpl1-3_Rep1_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("koiwa_657-4_cpl1-3_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: koiwa_657-4_cpl1-3_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: cpl3-1
Stock Code: CS6542
Growth Conditions:
StratificationSeeds were kept for 2 days at 4 celcius.
Sterilisation20 seconds in 70% Ethanol, then washed with sterile distilled water for three times. Then, seeds were suspended in 0.1% agar solution.
ProtocolThe seeds grown vertically for 10 days on media containing 1/4 Murashige and Skoog (MS) salts, 0.5 % sucrose, and 1.5% agar.
Plant Spacing50
Temperature25 °C average, 25 °C day, 25 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
Additional Organism Information:
Sample DescriptionWhole plant is used for sampling.
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:0.584804
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-ratio1.207431
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.679146
Spike_AFFX-r2-Bs-dap_5_signal71.716965
NoiseAvg:3.78,Std:0.14,Min:3.5,Max:4.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal36.372868
#P14204
Spike_AFFX-r2-Bs-phe_M_signal39.982849
Corner-Avg:12384,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal81.259636
Spike_AFFX-r2-Ec-bioB_3_signal86.487251
Spike_AFFX-r2-Bs-lys_M_signal35.675365
Spike_AFFX-r2-P1-cre_3_signal4496.526367
Spike_AFFX-r2-Bs-lys_3-5-ratio2.197251
Spike_AFFX-r2-Bs-dap_M_signal311.785431
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.854645
Spike_AFFX-r2-Ec-bioB_avg-signal73.084526
Spike_AFFX-r2-Bs-thr_avg-signal99.053314
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal997.723389
Spike_AFFX-r2-Bs-phe_5_signal22.502838
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1370.235596
RawQ3.068522
Spike_AFFX-r2-Bs-lys_5_signal29.154305
Signal(A)6.325181
%A35.751862
Signal(All)143.299362
Corner+Avg:468,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal260.490265
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal61.916138
Spike_AFFX-r2-Ec-bioD_avg-signal1183.979492
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.270935
Spike_AFFX-r2-Bs-lys_avg-signal42.963001
Spike_AFFX-r2-P1-cre_avg-signal4110.284668
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.977203
Spike_AFFX-r2-Bs-thr_3_signal176.577347
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-signal41.467274
Spike_AFFX-r2-Bs-dap_3_signal491.339935
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.373362
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal279.865326
#M451
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal64.059326
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.930770
Spike_AFFX-r2-Bs-thr_M_signal84.209740
Signal(P)225.763321
Spike_AFFX-r2-Bs-phe_3-5-ratio2.751481
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9316,Count:9
Spike_AFFX-r2-P1-cre_5_signal3724.042969
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8155
Signal(M)22.913921
BackgroundAvg:76.81,Std:0.71,Min:74.7,Max:78.6
Spike_AFFX-r2-Ec-bioC_avg-signal270.177795
Spike_AFFX-r2-Bs-dap_avg-signal291.614105
Spike_AFFX-r2-Bs-dap_3-5-ratio6.851098
Spike_AFFX-r2-Ec-bioB_5_signal51.506680
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.584804
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_657-5_cpl1-3_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 ("koiwa_657-5_cpl1-3_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: koiwa_657-5_cpl1-3_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: cpl3-1
Stock Code: CS6542
Growth Conditions:
StratificationSeeds were kept for 2 days at 4 celcius.
Sterilisation20 seconds in 70% Ethanol, then washed with sterile distilled water for three times. Then, seeds were suspended in 0.1% agar solution.
ProtocolThe seeds grown vertically for 10 days on media containing 1/4 Murashige and Skoog (MS) salts, 0.5 % sucrose, and 1.5% agar.
Plant Spacing50
Temperature25 °C average, 25 °C day, 25 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
Additional Organism Information:
Sample DescriptionWhole plant is used for sampling.
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:0.851773
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-ratio1.231443
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.554744
Spike_AFFX-r2-Bs-dap_5_signal115.555382
NoiseAvg:3.30,Std:0.11,Min:3.1,Max:3.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal39.264664
#P13745
Spike_AFFX-r2-Bs-phe_M_signal45.973942
Corner-Avg:10526,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal115.954079
Spike_AFFX-r2-Ec-bioB_3_signal86.290665
Spike_AFFX-r2-Bs-lys_M_signal25.545074
Spike_AFFX-r2-P1-cre_3_signal5251.773438
Spike_AFFX-r2-Bs-lys_3-5-ratio1.299268
Spike_AFFX-r2-Bs-dap_M_signal367.093109
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.283203
Spike_AFFX-r2-Ec-bioB_avg-signal85.915428
Spike_AFFX-r2-Bs-thr_avg-signal144.672897
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal932.903564
Spike_AFFX-r2-Bs-phe_5_signal28.928171
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1423.921997
RawQ2.792488
Spike_AFFX-r2-Bs-lys_5_signal35.193508
Signal(A)8.087140
%A37.536167
Signal(All)146.212616
Corner+Avg:400,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal318.256165
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal77.447289
Spike_AFFX-r2-Ec-bioD_avg-signal1178.412842
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.258659
Spike_AFFX-r2-Bs-lys_avg-signal35.488129
Spike_AFFX-r2-P1-cre_avg-signal4758.251953
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.205173
Spike_AFFX-r2-Bs-thr_3_signal246.707855
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-signal50.783138
Spike_AFFX-r2-Bs-dap_3_signal542.156311
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.526334
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal313.720428
#M503
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal45.725803
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.014458
Spike_AFFX-r2-Bs-thr_M_signal148.046188
Signal(P)236.652176
Spike_AFFX-r2-Bs-phe_3-5-ratio2.677227
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9666,Count:9
Spike_AFFX-r2-P1-cre_5_signal4264.730469
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8562
Signal(M)26.011057
BackgroundAvg:71.85,Std:0.66,Min:70.9,Max:74.0
Spike_AFFX-r2-Ec-bioC_avg-signal315.988281
Spike_AFFX-r2-Bs-dap_avg-signal341.601593
Spike_AFFX-r2-Bs-dap_3-5-ratio4.691744
Spike_AFFX-r2-Ec-bioB_5_signal55.501514
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.851773
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_657-6_cpl1-3_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("koiwa_657-6_cpl1-3_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

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

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

Hybridisation Protocol Information

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

BioSource 1 Information

BioSource Name: koiwa_657-6_cpl1-3_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: cpl3-1
Stock Code: CS6542
Growth Conditions:
StratificationSeeds were kept for 2 days at 4 celcius.
Sterilisation20 seconds in 70% Ethanol, then washed with sterile distilled water for three times. Then, seeds were suspended in 0.1% agar solution.
ProtocolThe seeds grown vertically for 10 days on media containing 1/4 Murashige and Skoog (MS) salts, 0.5 % sucrose, and 1.5% agar.
Plant Spacing50
Temperature25 °C average, 25 °C day, 25 °C night
Humidity100 % average, 100 % day, 100 % night
MediumMurashige & Skoog basal salt mixture
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole plant
Additional Organism Information:
Sample DescriptionWhole plant is used for sampling.
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:0.742118
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-ratio1.295202
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.567445
Spike_AFFX-r2-Bs-dap_5_signal71.263657
NoiseAvg:3.62,Std:0.13,Min:3.3,Max:4.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal32.564064
#P14021
Spike_AFFX-r2-Bs-phe_M_signal35.926640
Corner-Avg:10508,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal95.027382
Spike_AFFX-r2-Ec-bioB_3_signal87.465630
Spike_AFFX-r2-Bs-lys_M_signal21.878229
Spike_AFFX-r2-P1-cre_3_signal4828.977539
Spike_AFFX-r2-Bs-lys_3-5-ratio1.738181
Spike_AFFX-r2-Bs-dap_M_signal259.547089
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.236707
Spike_AFFX-r2-Ec-bioB_avg-signal79.431465
Spike_AFFX-r2-Bs-thr_avg-signal99.952263
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal842.593872
Spike_AFFX-r2-Bs-phe_5_signal24.903086
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1275.894165
RawQ3.064048
Spike_AFFX-r2-Bs-lys_5_signal28.505764
Signal(A)7.274989
%A36.256027
Signal(All)145.532928
Corner+Avg:394,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal291.177032
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal62.302589
Spike_AFFX-r2-Ec-bioD_avg-signal1059.244019
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.468655
Spike_AFFX-r2-Bs-lys_avg-signal33.310730
Spike_AFFX-r2-P1-cre_avg-signal4278.667480
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.275318
Spike_AFFX-r2-Bs-thr_3_signal170.528458
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-signal41.044106
Spike_AFFX-r2-Bs-dap_3_signal447.912323
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.514246
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal264.711090
#M519
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal49.548191
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.099980
Spike_AFFX-r2-Bs-thr_M_signal96.764267
Signal(P)231.531845
Spike_AFFX-r2-Bs-phe_3-5-ratio2.501802
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10124,Count:9
Spike_AFFX-r2-P1-cre_5_signal3728.357422
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8270
Signal(M)25.306345
BackgroundAvg:77.32,Std:1.16,Min:75.2,Max:81.0
Spike_AFFX-r2-Ec-bioC_avg-signal277.944061
Spike_AFFX-r2-Bs-dap_avg-signal259.574371
Spike_AFFX-r2-Bs-dap_3-5-ratio6.285284
Spike_AFFX-r2-Ec-bioB_5_signal55.801399
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.742118
NF1.000000
HZ4
Tau0.015000


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