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Experiment: Microarray Analyses of Arabidopsis cgl1 (complex glycan 1) Mutants and Genetic Interaction with stt3a (staurosporin&temperature-sensitive 3a)

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-547

We compare two Arabidopsis thaliana cgl1 alleles and report on genetic interaction with stt3a in double mutants. STT3a encodes a subunit of oligo-saccharyl-trans-ferase that affects efficiency of N-glycan transfer to nascent secretory proteins in the ER; cgl1 mutants lack N-acetyl-gluco-saminyl-trans-ferase-I activity and are unable to form complex N-glycans in the Golgi apparatus. In cgl1 C6, a point mutation affects the 3'-splice site of intron 14, resulting in frame shifts; and in cgl1-T, intron 11 fails to splice due to insertion of a T-DNA copy. Introgression of stt3a-2 did not restore complex glycan formation in cgl1 C6 or cgl1-T (Frank et.al.,2008). In this microarray experiment, Seeds were grown on 1/4 MS media supplemented with 0.5% sucrose and 0.8% agar in a growth chamber under long-day photoperiod (16-hr light, 8-hr darkness) at 24 ± 2°C for 10 days. Then, seedlings were transferred into soil and grown three more weeks in a growth chamber at 25 ± 2ºC under long-day photoperiod at a light intensity of 40 μmol m-2s-1. Then, shoots from 5 plants were pooled and total RNAs were extracted according to Chomczynski (1993).

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:
Country:
 
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_design
Number of Slides:14
 
Experimental Parameters:
parametergene_knock_out
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: koiwa: Microarray Analyses of Arabidopsis cgl1 (complex glycan 1) Mutants and Genetic Interaction with stt3a (staurosporin&temperature-sensitive 3a)

Slide: koiwa_547-1_Col-0_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_547-1_Col-0_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_547-1_Col-0_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N6673
Age: 31 days old
Growth Conditions:
StratificationCold treatment for 2 days.
SterilisationWashed with 70% EtOH for 10 seconds and rinsed with distilled water for three times.
ProtocolSeeds were grown on 1/4 MS media supplemented with 0.5% sucrose and 0.8% agar in a growth chamber under long-day photoperiod (16-hr light, 8-hr darkness) at 24 ± 2°C for 10 days. Then, seedlings were transferred into soil and grown three more weeks in a growth chamber at 25 ± 2°C under long-day photoperiod at a light intensity of 40 µmol m-2s-1.
Soil ConstituentsSunGro Metromix 300: Contains 30-40% horticultural grade Vermiculite, Bark, Canadian Sphangum peat moss, horticultural grade Perlite, bark ash, Dolomitic limestone, and a wetting agent.
Plant Spacing5 in each pot
waterin every 2 days
Temperature23 °C average, 23 °C day, 23 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige and Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 40µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: shoot
Additional Organism Information:
Sample DescriptionRNA was extracted from shoots pooled from 5 plants
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:0.831528
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-ratio1.229972
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.717437
Spike_AFFX-r2-Bs-dap_5_signal205.370193
NoiseAvg:2.17,Std:0.06,Min:1.9,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal85.321236
#P14610
Spike_AFFX-r2-Bs-phe_M_signal85.600281
Corner-Avg:7144,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal133.480072
Spike_AFFX-r2-Ec-bioB_3_signal80.381310
Spike_AFFX-r2-Bs-lys_M_signal37.116535
Spike_AFFX-r2-P1-cre_3_signal6614.101074
Spike_AFFX-r2-Bs-lys_3-5-ratio1.390939
Spike_AFFX-r2-Bs-dap_M_signal333.996948
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.348667
Spike_AFFX-r2-Ec-bioB_avg-signal108.633629
Spike_AFFX-r2-Bs-thr_avg-signal186.057785
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1111.973267
Spike_AFFX-r2-Bs-phe_5_signal85.599457
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1650.029053
RawQ2.117738
Spike_AFFX-r2-Bs-lys_5_signal47.481792
Signal(A)5.121679
%A33.945637
Signal(All)147.009735
Corner+Avg:88,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal377.507446
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal79.409050
Spike_AFFX-r2-Ec-bioD_avg-signal1381.001221
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.050858
Spike_AFFX-r2-Bs-lys_avg-signal50.214199
Spike_AFFX-r2-P1-cre_avg-signal5995.769531
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.003507
Spike_AFFX-r2-Bs-thr_3_signal285.712433
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-signal83.536263
Spike_AFFX-r2-Bs-dap_3_signal497.245514
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.483875
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal336.389954
#M457
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal66.044266
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.122232
Spike_AFFX-r2-Bs-thr_M_signal187.139679
Signal(P)226.241180
Spike_AFFX-r2-Bs-phe_3-5-ratio0.927682
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4636,Count:9
Spike_AFFX-r2-P1-cre_5_signal5377.438477
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7743
Signal(M)18.054691
BackgroundAvg:50.37,Std:0.45,Min:49.7,Max:52.0
Spike_AFFX-r2-Ec-bioC_avg-signal356.948700
Spike_AFFX-r2-Bs-dap_avg-signal345.537567
Spike_AFFX-r2-Bs-dap_3-5-ratio2.421216
Spike_AFFX-r2-Ec-bioB_5_signal112.039497
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.831528
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_547-2_Col-0_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_547-2_Col-0_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_547-2_Col-0_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N6673
Age: 31 days old
Growth Conditions:
StratificationCold treatment for 2 days.
SterilisationWashed with 70% EtOH for 10 seconds and rinsed with distilled water for three times.
ProtocolSeeds were grown on 1/4 MS media supplemented with 0.5% sucrose and 0.8% agar in a growth chamber under long-day photoperiod (16-hr light, 8-hr darkness) at 24 ± 2°C for 10 days. Then, seedlings were transferred into soil and grown three more weeks in a growth chamber at 25 ± 2°C under long-day photoperiod at a light intensity of 40 µmol m-2s-1.
Soil ConstituentsSunGro Metromix 300: Contains 30-40% horticultural grade Vermiculite, Bark, Canadian Sphangum peat moss, horticultural grade Perlite, bark ash, Dolomitic limestone, and a wetting agent.
Plant Spacing5 in each pot
waterin every 2 days
Temperature23 °C average, 23 °C day, 23 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige and Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 40µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: shoot
Additional Organism Information:
Sample DescriptionRNA was extracted from shoots pooled from 5 plants
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:0.90496
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-ratio1.318648
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.951167
Spike_AFFX-r2-Bs-dap_5_signal187.519119
NoiseAvg:1.93,Std:0.08,Min:1.7,Max:2.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal77.915001
#P14819
Spike_AFFX-r2-Bs-phe_M_signal89.802917
Corner-Avg:8191,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal153.698105
Spike_AFFX-r2-Ec-bioB_3_signal121.159279
Spike_AFFX-r2-Bs-lys_M_signal31.629978
Spike_AFFX-r2-P1-cre_3_signal8518.637695
Spike_AFFX-r2-Bs-lys_3-5-ratio1.391042
Spike_AFFX-r2-Bs-dap_M_signal341.976471
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.444081
Spike_AFFX-r2-Ec-bioB_avg-signal134.078995
Spike_AFFX-r2-Bs-thr_avg-signal170.160919
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1413.585327
Spike_AFFX-r2-Bs-phe_5_signal93.422691
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2031.695068
RawQ1.969346
Spike_AFFX-r2-Bs-lys_5_signal36.560925
Signal(A)4.344523
%A33.195965
Signal(All)148.624054
Corner+Avg:102,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal498.875153
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal102.420998
Spike_AFFX-r2-Ec-bioD_avg-signal1722.640137
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.967117
Spike_AFFX-r2-Bs-lys_avg-signal39.682892
Spike_AFFX-r2-P1-cre_avg-signal7489.384277
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_signal268.345581
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-signal95.215538
Spike_AFFX-r2-Bs-dap_3_signal490.265015
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.437264
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal455.050446
#M419
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal50.857777
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.096307
Spike_AFFX-r2-Bs-thr_M_signal164.222183
Signal(P)226.123154
Spike_AFFX-r2-Bs-phe_3-5-ratio1.096318
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5230,Count:9
Spike_AFFX-r2-P1-cre_5_signal6460.130859
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7572
Signal(M)15.033341
BackgroundAvg:48.60,Std:0.45,Min:47.5,Max:50.0
Spike_AFFX-r2-Ec-bioC_avg-signal476.962799
Spike_AFFX-r2-Bs-dap_avg-signal339.920197
Spike_AFFX-r2-Bs-dap_3-5-ratio2.614480
Spike_AFFX-r2-Ec-bioB_5_signal127.379608
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.904960
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_547-3_Col-0_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_547-3_Col-0_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_547-3_Col-0_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N6673
Age: 31 days old
Growth Conditions:
StratificationCold treatment for 2 days.
SterilisationWashed with 70% EtOH for 10 seconds and rinsed with distilled water for three times.
ProtocolSeeds were grown on 1/4 MS media supplemented with 0.5% sucrose and 0.8% agar in a growth chamber under long-day photoperiod (16-hr light, 8-hr darkness) at 24 ± 2°C for 10 days. Then, seedlings were transferred into soil and grown three more weeks in a growth chamber at 25 ± 2°C under long-day photoperiod at a light intensity of 40 µmol m-2s-1.
Soil ConstituentsSunGro Metromix 300: Contains 30-40% horticultural grade Vermiculite, Bark, Canadian Sphangum peat moss, horticultural grade Perlite, bark ash, Dolomitic limestone, and a wetting agent.
Plant Spacing5 in each pot
waterin every 2 days
Temperature23 °C average, 23 °C day, 23 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige and Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 40µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: shoot
Additional Organism Information:
Sample DescriptionRNA was extracted from shoots pooled from 5 plants
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:0.842772
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-ratio1.207757
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.840225
Spike_AFFX-r2-Bs-dap_5_signal139.722366
NoiseAvg:1.95,Std:0.06,Min:1.7,Max:2.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal63.306309
#P14981
Spike_AFFX-r2-Bs-phe_M_signal88.722771
Corner-Avg:6840,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal133.524384
Spike_AFFX-r2-Ec-bioB_3_signal81.702072
Spike_AFFX-r2-Bs-lys_M_signal40.203838
Spike_AFFX-r2-P1-cre_3_signal6305.290039
Spike_AFFX-r2-Bs-lys_3-5-ratio0.946030
Spike_AFFX-r2-Bs-dap_M_signal357.134308
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.199111
Spike_AFFX-r2-Ec-bioB_avg-signal104.154938
Spike_AFFX-r2-Bs-thr_avg-signal183.664368
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1059.768188
Spike_AFFX-r2-Bs-phe_5_signal92.041191
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1651.247559
RawQ1.996280
Spike_AFFX-r2-Bs-lys_5_signal42.916786
Signal(A)4.157609
%A32.713722
Signal(All)147.666916
Corner+Avg:74,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal385.125763
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal93.103310
Spike_AFFX-r2-Ec-bioD_avg-signal1355.507813
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.677338
Spike_AFFX-r2-Bs-lys_avg-signal41.240391
Spike_AFFX-r2-P1-cre_avg-signal5762.975586
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.608943
Spike_AFFX-r2-Bs-thr_3_signal329.136505
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-signal91.289093
Spike_AFFX-r2-Bs-dap_3_signal410.504578
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.558121
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal359.481293
#M367
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal40.600548
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.071337
Spike_AFFX-r2-Bs-thr_M_signal158.550262
Signal(P)222.390472
Spike_AFFX-r2-Bs-phe_3-5-ratio1.011540
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4849,Count:9
Spike_AFFX-r2-P1-cre_5_signal5220.660645
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7462
Signal(M)15.330653
BackgroundAvg:47.99,Std:0.54,Min:46.8,Max:49.1
Spike_AFFX-r2-Ec-bioC_avg-signal372.303528
Spike_AFFX-r2-Bs-dap_avg-signal302.453766
Spike_AFFX-r2-Bs-dap_3-5-ratio2.938002
Spike_AFFX-r2-Ec-bioB_5_signal97.238365
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.842772
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_547-4_cgl-C6_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_547-4_cgl-C6_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_547-4_cgl-C6_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: cgl1-2
Stock Code: N16366
Age: 31 days old
Growth Conditions:
StratificationCold treatment for 2 days.
SterilisationWashed with 70% EtOH for 10 seconds and rinsed with distilled water for three times.
ProtocolSeeds were grown on 1/4 MS media supplemented with 0.5% sucrose and 0.8% agar in a growth chamber under long-day photoperiod (16-hr light, 8-hr darkness) at 24 ± 2°C for 10 days. Then, seedlings were transferred into soil and grown three more weeks in a growth chamber at 25 ± 2°C under long-day photoperiod at a light intensity of 40 µmol m-2s-1.
Soil ConstituentsSunGro Metromix 300: Contains 30-40% horticultural grade Vermiculite, Bark, Canadian Sphangum peat moss, horticultural grade Perlite, bark ash, Dolomitic limestone, and a wetting agent.
Plant Spacing5 in each pot
waterin every 2 days
Temperature23 °C average, 23 °C day, 23 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige and Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 40µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: shoot
Additional Organism Information:
Sample DescriptionRNA was extracted from shoots pooled from 5 plants
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:0.393894
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-ratio1.220923
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.778017
Spike_AFFX-r2-Bs-dap_5_signal110.921570
NoiseAvg:2.39,Std:0.06,Min:2.2,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal54.991642
#P16094
Spike_AFFX-r2-Bs-phe_M_signal58.570190
Corner-Avg:8861,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal81.216476
Spike_AFFX-r2-Ec-bioB_3_signal39.657497
Spike_AFFX-r2-Bs-lys_M_signal16.967585
Spike_AFFX-r2-P1-cre_3_signal3061.835693
Spike_AFFX-r2-Bs-lys_3-5-ratio1.008098
Spike_AFFX-r2-Bs-dap_M_signal268.812347
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.631033
Spike_AFFX-r2-Ec-bioB_avg-signal57.282177
Spike_AFFX-r2-Bs-thr_avg-signal123.077721
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal474.262421
Spike_AFFX-r2-Bs-phe_5_signal69.681587
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal800.860352
RawQ2.056874
Spike_AFFX-r2-Bs-lys_5_signal44.506454
Signal(A)2.492566
%A27.961420
Signal(All)137.096420
Corner+Avg:104,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal219.315231
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal73.719521
Spike_AFFX-r2-Ec-bioD_avg-signal637.561401
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.556770
Spike_AFFX-r2-Bs-lys_avg-signal35.446964
Spike_AFFX-r2-P1-cre_avg-signal2784.819824
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.481806
Spike_AFFX-r2-Bs-thr_3_signal199.676483
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-signal67.323761
Spike_AFFX-r2-Bs-dap_3_signal320.559357
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.688644
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal193.631378
#M338
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal44.866852
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.132643
Spike_AFFX-r2-Bs-thr_M_signal114.565041
Signal(P)193.098816
Spike_AFFX-r2-Bs-phe_3-5-ratio1.057948
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6694,Count:9
Spike_AFFX-r2-P1-cre_5_signal2507.803711
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6378
Signal(M)10.472297
BackgroundAvg:53.97,Std:0.44,Min:52.8,Max:55.0
Spike_AFFX-r2-Ec-bioC_avg-signal206.473297
Spike_AFFX-r2-Bs-dap_avg-signal233.431091
Spike_AFFX-r2-Bs-dap_3-5-ratio2.889964
Spike_AFFX-r2-Ec-bioB_5_signal50.972549
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.393894
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_547-5_cgl-T_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 ("koiwa_547-5_cgl-T_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_547-5_cgl-T_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_073650 homozygous
Stock Code: N16367
Genetic Background: Col-0 (Columbia, N60000)
Age: 31 days old
Growth Conditions:
StratificationCold treatment for 2 days.
SterilisationWashed with 70% EtOH for 10 seconds and rinsed with distilled water for three times.
ProtocolSeeds were grown on 1/4 MS media supplemented with 0.5% sucrose and 0.8% agar in a growth chamber under long-day photoperiod (16-hr light, 8-hr darkness) at 24 ± 2°C for 10 days. Then, seedlings were transferred into soil and grown three more weeks in a growth chamber at 25 ± 2°C under long-day photoperiod at a light intensity of 40 µmol m-2s-1.
Soil ConstituentsSunGro Metromix 300: Contains 30-40% horticultural grade Vermiculite, Bark, Canadian Sphangum peat moss, horticultural grade Perlite, bark ash, Dolomitic limestone, and a wetting agent.
Plant Spacing5 in each pot
waterin every 2 days
Temperature23 °C average, 23 °C day, 23 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige and Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 40µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: shoot
Additional Organism Information:
Sample DescriptionRNA was extracted from shoots pooled from 5 plants
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:0.829883
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-ratio1.218716
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.012860
Spike_AFFX-r2-Bs-dap_5_signal196.754791
NoiseAvg:2.03,Std:0.05,Min:1.9,Max:2.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal63.193478
#P14987
Spike_AFFX-r2-Bs-phe_M_signal84.809059
Corner-Avg:8428,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal163.048981
Spike_AFFX-r2-Ec-bioB_3_signal137.702866
Spike_AFFX-r2-Bs-lys_M_signal50.827408
Spike_AFFX-r2-P1-cre_3_signal7902.449707
Spike_AFFX-r2-Bs-lys_3-5-ratio1.436603
Spike_AFFX-r2-Bs-dap_M_signal334.843658
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.514949
Spike_AFFX-r2-Ec-bioB_avg-signal145.568756
Spike_AFFX-r2-Bs-thr_avg-signal168.729507
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1635.858521
Spike_AFFX-r2-Bs-phe_5_signal93.660622
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2070.289551
RawQ2.111096
Spike_AFFX-r2-Bs-lys_5_signal46.668613
Signal(A)4.475974
%A32.560280
Signal(All)148.471680
Corner+Avg:93,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal520.855957
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal87.355446
Spike_AFFX-r2-Ec-bioD_avg-signal1853.073975
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.703636
Spike_AFFX-r2-Bs-lys_avg-signal54.846767
Spike_AFFX-r2-P1-cre_avg-signal7193.345703
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.736081
Spike_AFFX-r2-Bs-thr_3_signal285.315338
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-signal88.608376
Spike_AFFX-r2-Bs-dap_3_signal539.824585
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.265568
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal453.192963
#M396
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal67.044281
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.149303
Spike_AFFX-r2-Bs-thr_M_signal157.679703
Signal(P)223.317535
Spike_AFFX-r2-Bs-phe_3-5-ratio0.932681
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5765,Count:9
Spike_AFFX-r2-P1-cre_5_signal6484.241211
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7427
Signal(M)16.504930
BackgroundAvg:51.92,Std:0.34,Min:50.6,Max:52.9
Spike_AFFX-r2-Ec-bioC_avg-signal487.024475
Spike_AFFX-r2-Bs-dap_avg-signal357.140991
Spike_AFFX-r2-Bs-dap_3-5-ratio2.743641
Spike_AFFX-r2-Ec-bioB_5_signal135.954437
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.829883
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_547-6_cgl-T_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_547-6_cgl-T_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_547-6_cgl-T_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_073650 homozygous
Stock Code: N16367
Genetic Background: Col-0 (Columbia, N60000)
Age: 31 days old
Growth Conditions:
StratificationCold treatment for 2 days.
SterilisationWashed with 70% EtOH for 10 seconds and rinsed with distilled water for three times.
ProtocolSeeds were grown on 1/4 MS media supplemented with 0.5% sucrose and 0.8% agar in a growth chamber under long-day photoperiod (16-hr light, 8-hr darkness) at 24 ± 2°C for 10 days. Then, seedlings were transferred into soil and grown three more weeks in a growth chamber at 25 ± 2°C under long-day photoperiod at a light intensity of 40 µmol m-2s-1.
Soil ConstituentsSunGro Metromix 300: Contains 30-40% horticultural grade Vermiculite, Bark, Canadian Sphangum peat moss, horticultural grade Perlite, bark ash, Dolomitic limestone, and a wetting agent.
Plant Spacing5 in each pot
waterin every 2 days
Temperature23 °C average, 23 °C day, 23 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige and Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 40µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: shoot
Additional Organism Information:
Sample DescriptionRNA was extracted from shoots pooled from 5 plants
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:0.965639
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-ratio1.291014
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.026431
Spike_AFFX-r2-Bs-dap_5_signal156.519028
NoiseAvg:1.93,Std:0.06,Min:1.7,Max:2.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal66.937462
#P14794
Spike_AFFX-r2-Bs-phe_M_signal75.520332
Corner-Avg:8138,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal179.233810
Spike_AFFX-r2-Ec-bioB_3_signal122.474960
Spike_AFFX-r2-Bs-lys_M_signal44.283646
Spike_AFFX-r2-P1-cre_3_signal8209.136719
Spike_AFFX-r2-Bs-lys_3-5-ratio1.468705
Spike_AFFX-r2-Bs-dap_M_signal355.721161
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.599145
Spike_AFFX-r2-Ec-bioB_avg-signal140.343307
Spike_AFFX-r2-Bs-thr_avg-signal168.649414
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1390.644653
Spike_AFFX-r2-Bs-phe_5_signal77.781372
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2026.650635
RawQ2.029520
Spike_AFFX-r2-Bs-lys_5_signal40.151310
Signal(A)4.743270
%A33.331871
Signal(All)147.863663
Corner+Avg:88,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal491.765961
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal82.557915
Spike_AFFX-r2-Ec-bioD_avg-signal1708.647705
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.857521
Spike_AFFX-r2-Bs-lys_avg-signal47.801800
Spike_AFFX-r2-P1-cre_avg-signal7283.905273
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.810609
Spike_AFFX-r2-Bs-thr_3_signal307.855133
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal78.619873
Spike_AFFX-r2-Bs-dap_3_signal389.974304
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.457346
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal443.497467
#M413
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal58.970444
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.108836
Spike_AFFX-r2-Bs-thr_M_signal131.155640
Signal(P)225.081482
Spike_AFFX-r2-Bs-phe_3-5-ratio1.061410
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5578,Count:9
Spike_AFFX-r2-P1-cre_5_signal6358.674316
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7603
Signal(M)16.589624
BackgroundAvg:49.19,Std:0.28,Min:48.2,Max:49.9
Spike_AFFX-r2-Ec-bioC_avg-signal467.631714
Spike_AFFX-r2-Bs-dap_avg-signal300.738159
Spike_AFFX-r2-Bs-dap_3-5-ratio2.491546
Spike_AFFX-r2-Ec-bioB_5_signal119.321129
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.965639
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_547-7_cgl-T_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_547-7_cgl-T_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_547-7_cgl-T_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_073650 homozygous
Stock Code: N16367
Genetic Background: Col-0 (Columbia, N60000)
Age: 31 days old
Growth Conditions:
StratificationCold treatment for 2 days.
SterilisationWashed with 70% EtOH for 10 seconds and rinsed with distilled water for three times.
ProtocolSeeds were grown on 1/4 MS media supplemented with 0.5% sucrose and 0.8% agar in a growth chamber under long-day photoperiod (16-hr light, 8-hr darkness) at 24 ± 2°C for 10 days. Then, seedlings were transferred into soil and grown three more weeks in a growth chamber at 25 ± 2°C under long-day photoperiod at a light intensity of 40 µmol m-2s-1.
Soil ConstituentsSunGro Metromix 300: Contains 30-40% horticultural grade Vermiculite, Bark, Canadian Sphangum peat moss, horticultural grade Perlite, bark ash, Dolomitic limestone, and a wetting agent.
Plant Spacing5 in each pot
waterin every 2 days
Temperature23 °C average, 23 °C day, 23 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige and Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 40µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: shoot
Additional Organism Information:
Sample DescriptionRNA was extracted from shoots pooled from 5 plants
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:0.469563
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-ratio1.133321
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.876130
Spike_AFFX-r2-Bs-dap_5_signal88.831543
NoiseAvg:2.20,Std:0.06,Min:2.0,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal61.329231
#P16068
Spike_AFFX-r2-Bs-phe_M_signal51.205067
Corner-Avg:8105,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal67.811104
Spike_AFFX-r2-Ec-bioB_3_signal52.128868
Spike_AFFX-r2-Bs-lys_M_signal19.705355
Spike_AFFX-r2-P1-cre_3_signal2780.001709
Spike_AFFX-r2-Bs-lys_3-5-ratio2.079130
Spike_AFFX-r2-Bs-dap_M_signal196.546570
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.797439
Spike_AFFX-r2-Ec-bioB_avg-signal59.812988
Spike_AFFX-r2-Bs-thr_avg-signal147.819382
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal464.363708
Spike_AFFX-r2-Bs-phe_5_signal63.323929
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal816.460571
RawQ2.007296
Spike_AFFX-r2-Bs-lys_5_signal32.328686
Signal(A)2.547461
%A28.066637
Signal(All)137.651291
Corner+Avg:89,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal197.719376
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal65.108810
Spike_AFFX-r2-Ec-bioD_avg-signal640.412109
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.442787
Spike_AFFX-r2-Bs-lys_avg-signal39.749859
Spike_AFFX-r2-P1-cre_avg-signal2616.485840
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.490574
Spike_AFFX-r2-Bs-thr_3_signal232.894028
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-signal59.879269
Spike_AFFX-r2-Bs-dap_3_signal276.840820
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.758235
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal198.729782
#M340
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal67.215530
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.994916
Spike_AFFX-r2-Bs-thr_M_signal149.234879
Signal(P)194.176300
Spike_AFFX-r2-Bs-phe_3-5-ratio1.028187
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5375,Count:9
Spike_AFFX-r2-P1-cre_5_signal2452.969727
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6402
Signal(M)10.271211
BackgroundAvg:52.70,Std:0.41,Min:51.8,Max:54.0
Spike_AFFX-r2-Ec-bioC_avg-signal198.224579
Spike_AFFX-r2-Bs-dap_avg-signal187.406311
Spike_AFFX-r2-Bs-dap_3-5-ratio3.116470
Spike_AFFX-r2-Ec-bioB_5_signal59.498985
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.469563
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_548-1_stt3a_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 ("koiwa_548-1_stt3a_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_548-1_stt3a_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: staurosporin and temperature sensitive 3-like a
Stock Code: N800052
Genetic Background: N60000
Age: 31 days old
Growth Conditions:
StratificationCold treatment for 2 days.
SterilisationWashed with 70% EtOH for 10 seconds and rinsed with distilled water for three times.
ProtocolSeeds were grown on 1/4 MS media supplemented with 0.5% sucrose and 0.8% agar in a growth chamber under long-day photoperiod (16-hr light, 8-hr darkness) at 24 ± 2°C for 10 days. Then, seedlings were transferred into soil and grown three more weeks in a growth chamber at 25 ± 2°C under long-day photoperiod at a light intensity of 40 µmol m-2s-1.
Soil ConstituentsSunGro Metromix 300: Contains 30-40% horticultural grade Vermiculite, Bark, Canadian Sphangum peat moss, horticultural grade Perlite, bark ash, Dolomitic limestone, and a wetting agent.
Plant Spacing5 in each pot
waterin every 2 days
Temperature23 °C average, 23 °C day, 23 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige and Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 40µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: shoot
Additional Organism Information:
Sample DescriptionRNA was extracted from shoots pooled from 5 plants
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:0.455088
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-ratio1.203326
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.986049
Spike_AFFX-r2-Bs-dap_5_signal83.211029
NoiseAvg:2.34,Std:0.05,Min:2.2,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal41.128567
#P15708
Spike_AFFX-r2-Bs-phe_M_signal39.183842
Corner-Avg:7693,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal74.299431
Spike_AFFX-r2-Ec-bioB_3_signal52.875904
Spike_AFFX-r2-Bs-lys_M_signal13.114424
Spike_AFFX-r2-P1-cre_3_signal3174.698975
Spike_AFFX-r2-Bs-lys_3-5-ratio1.324237
Spike_AFFX-r2-Bs-dap_M_signal209.892303
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.779584
Spike_AFFX-r2-Ec-bioB_avg-signal60.266460
Spike_AFFX-r2-Bs-thr_avg-signal84.123283
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal499.588867
Spike_AFFX-r2-Bs-phe_5_signal48.047382
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal853.189087
RawQ2.220354
Spike_AFFX-r2-Bs-lys_5_signal26.037399
Signal(A)2.669505
%A29.684349
Signal(All)139.333344
Corner+Avg:83,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal227.354828
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal51.104572
Spike_AFFX-r2-Ec-bioD_avg-signal676.388977
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.864532
Spike_AFFX-r2-Bs-lys_avg-signal24.543833
Spike_AFFX-r2-P1-cre_avg-signal2906.485107
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.451118
Spike_AFFX-r2-Bs-thr_3_signal114.320290
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-signal46.111935
Spike_AFFX-r2-Bs-dap_3_signal242.662506
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.707782
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal205.118225
#M331
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal34.479675
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.108409
Spike_AFFX-r2-Bs-thr_M_signal96.920975
Signal(P)200.942429
Spike_AFFX-r2-Bs-phe_3-5-ratio1.063629
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6471,Count:9
Spike_AFFX-r2-P1-cre_5_signal2638.271240
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6771
Signal(M)11.222002
BackgroundAvg:76.71,Std:0.46,Min:74.9,Max:77.7
Spike_AFFX-r2-Ec-bioC_avg-signal216.236526
Spike_AFFX-r2-Bs-dap_avg-signal178.588623
Spike_AFFX-r2-Bs-dap_3-5-ratio2.916230
Spike_AFFX-r2-Ec-bioB_5_signal53.624035
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.455088
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_548-2_stt3a_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 ("koiwa_548-2_stt3a_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_548-2_stt3a_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: staurosporin and temperature sensitive 3-like a
Stock Code: N800052
Genetic Background: N60000
Age: 31 days old
Growth Conditions:
StratificationCold treatment for 2 days.
SterilisationWashed with 70% EtOH for 10 seconds and rinsed with distilled water for three times.
ProtocolSeeds were grown on 1/4 MS media supplemented with 0.5% sucrose and 0.8% agar in a growth chamber under long-day photoperiod (16-hr light, 8-hr darkness) at 24 ± 2°C for 10 days. Then, seedlings were transferred into soil and grown three more weeks in a growth chamber at 25 ± 2°C under long-day photoperiod at a light intensity of 40 µmol m-2s-1.
Soil ConstituentsSunGro Metromix 300: Contains 30-40% horticultural grade Vermiculite, Bark, Canadian Sphangum peat moss, horticultural grade Perlite, bark ash, Dolomitic limestone, and a wetting agent.
Plant Spacing5 in each pot
waterin every 2 days
Temperature23 °C average, 23 °C day, 23 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige and Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 40µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: shoot
Additional Organism Information:
Sample DescriptionRNA was extracted from shoots pooled from 5 plants
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:0.713551
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-ratio1.199295
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.891953
Spike_AFFX-r2-Bs-dap_5_signal108.142853
NoiseAvg:2.08,Std:0.08,Min:1.9,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal45.834984
#P15173
Spike_AFFX-r2-Bs-phe_M_signal49.488380
Corner-Avg:7194,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal116.631203
Spike_AFFX-r2-Ec-bioB_3_signal93.383545
Spike_AFFX-r2-Bs-lys_M_signal24.189543
Spike_AFFX-r2-P1-cre_3_signal5846.514648
Spike_AFFX-r2-Bs-lys_3-5-ratio2.657274
Spike_AFFX-r2-Bs-dap_M_signal232.650833
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.524631
Spike_AFFX-r2-Ec-bioB_avg-signal104.903435
Spike_AFFX-r2-Bs-thr_avg-signal106.348869
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1008.077820
Spike_AFFX-r2-Bs-phe_5_signal59.981041
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1561.096680
RawQ2.110995
Spike_AFFX-r2-Bs-lys_5_signal27.368433
Signal(A)3.861912
%A31.880754
Signal(All)146.435333
Corner+Avg:81,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal401.830475
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal62.183643
Spike_AFFX-r2-Ec-bioD_avg-signal1284.587280
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.519073
Spike_AFFX-r2-Bs-lys_avg-signal41.427807
Spike_AFFX-r2-P1-cre_avg-signal5360.738281
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_signal161.551392
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal57.217693
Spike_AFFX-r2-Bs-dap_3_signal352.765472
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.548587
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal337.116730
#M365
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal72.725441
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.191962
Spike_AFFX-r2-Bs-thr_M_signal111.660210
Signal(P)217.948517
Spike_AFFX-r2-Bs-phe_3-5-ratio1.036722
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5343,Count:9
Spike_AFFX-r2-P1-cre_5_signal4874.961426
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7272
Signal(M)14.173590
BackgroundAvg:51.97,Std:0.16,Min:51.4,Max:52.3
Spike_AFFX-r2-Ec-bioC_avg-signal369.473602
Spike_AFFX-r2-Bs-dap_avg-signal231.186401
Spike_AFFX-r2-Bs-dap_3-5-ratio3.262032
Spike_AFFX-r2-Ec-bioB_5_signal104.695549
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.713551
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_548-3_stt3a_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_548-3_stt3a_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_548-3_stt3a_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: staurosporin and temperature sensitive 3-like a
Stock Code: N800052
Genetic Background: N60000
Age: 31 days old
Growth Conditions:
StratificationCold treatment for 2 days.
SterilisationWashed with 70% EtOH for 10 seconds and rinsed with distilled water for three times.
ProtocolSeeds were grown on 1/4 MS media supplemented with 0.5% sucrose and 0.8% agar in a growth chamber under long-day photoperiod (16-hr light, 8-hr darkness) at 24 ± 2°C for 10 days. Then, seedlings were transferred into soil and grown three more weeks in a growth chamber at 25 ± 2°C under long-day photoperiod at a light intensity of 40 µmol m-2s-1.
Soil ConstituentsSunGro Metromix 300: Contains 30-40% horticultural grade Vermiculite, Bark, Canadian Sphangum peat moss, horticultural grade Perlite, bark ash, Dolomitic limestone, and a wetting agent.
Plant Spacing5 in each pot
waterin every 2 days
Temperature23 °C average, 23 °C day, 23 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige and Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 40µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: shoot
Additional Organism Information:
Sample DescriptionRNA was extracted from shoots pooled from 5 plants
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.077219
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-ratio1.284966
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.804010
Spike_AFFX-r2-Bs-dap_5_signal191.383636
NoiseAvg:1.95,Std:0.06,Min:1.8,Max:2.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal80.073486
#P14148
Spike_AFFX-r2-Bs-phe_M_signal107.658264
Corner-Avg:7129,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal167.040344
Spike_AFFX-r2-Ec-bioB_3_signal114.579735
Spike_AFFX-r2-Bs-lys_M_signal44.214317
Spike_AFFX-r2-P1-cre_3_signal8031.518066
Spike_AFFX-r2-Bs-lys_3-5-ratio1.751696
Spike_AFFX-r2-Bs-dap_M_signal388.413757
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.259794
Spike_AFFX-r2-Ec-bioB_avg-signal141.376831
Spike_AFFX-r2-Bs-thr_avg-signal220.361130
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1203.511108
Spike_AFFX-r2-Bs-phe_5_signal100.074913
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1898.718750
RawQ1.916574
Spike_AFFX-r2-Bs-lys_5_signal49.726006
Signal(A)6.011100
%A35.699253
Signal(All)151.504135
Corner+Avg:88,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal574.281250
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal105.776718
Spike_AFFX-r2-Ec-bioD_avg-signal1551.114990
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.025429
Spike_AFFX-r2-Bs-lys_avg-signal60.348389
Spike_AFFX-r2-P1-cre_avg-signal7140.945313
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_signal341.096527
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-signal104.503296
Spike_AFFX-r2-Bs-dap_3_signal552.433777
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.577650
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal465.016754
#M519
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal87.104828
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.234969
Spike_AFFX-r2-Bs-thr_M_signal239.913361
Signal(P)240.036819
Spike_AFFX-r2-Bs-phe_3-5-ratio1.056975
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5560,Count:9
Spike_AFFX-r2-P1-cre_5_signal6250.372559
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8143
Signal(M)20.847456
BackgroundAvg:47.60,Std:0.29,Min:46.7,Max:48.6
Spike_AFFX-r2-Ec-bioC_avg-signal519.648987
Spike_AFFX-r2-Bs-dap_avg-signal377.410400
Spike_AFFX-r2-Bs-dap_3-5-ratio2.886526
Spike_AFFX-r2-Ec-bioB_5_signal142.510406
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.077219
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_548-4_stt3a-cglC6_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 ("koiwa_548-4_stt3a-cglC6_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_548-4_stt3a-cglC6_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: stt3a cgl C6
Stock Code:
Age: 31 days old
Growth Conditions:
StratificationCold treatment for 2 days.
SterilisationWashed with 70% EtOH for 10 seconds and rinsed with distilled water for three times.
ProtocolSeeds were grown on 1/4 MS media supplemented with 0.5% sucrose and 0.8% agar in a growth chamber under long-day photoperiod (16-hr light, 8-hr darkness) at 24 ± 2°C for 10 days. Then, seedlings were transferred into soil and grown three more weeks in a growth chamber at 25 ± 2°C under long-day photoperiod at a light intensity of 40 µmol m-2s-1.
Soil ConstituentsSunGro Metromix 300: Contains 30-40% horticultural grade Vermiculite, Bark, Canadian Sphangum peat moss, horticultural grade Perlite, bark ash, Dolomitic limestone, and a wetting agent.
Plant Spacing5 in each pot
waterin every 2 days
Temperature23 °C average, 23 °C day, 23 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige and Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 40µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: shoot
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:0.716042
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-ratio1.152158
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.861962
Spike_AFFX-r2-Bs-dap_5_signal232.347122
NoiseAvg:1.96,Std:0.07,Min:1.8,Max:2.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal125.089592
#P13807
Spike_AFFX-r2-Bs-phe_M_signal137.860825
Corner-Avg:8774,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal99.096992
Spike_AFFX-r2-Ec-bioB_3_signal83.228378
Spike_AFFX-r2-Bs-lys_M_signal45.418949
Spike_AFFX-r2-P1-cre_3_signal4959.133301
Spike_AFFX-r2-Bs-lys_3-5-ratio1.098783
Spike_AFFX-r2-Bs-dap_M_signal605.560974
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.805913
Spike_AFFX-r2-Ec-bioB_avg-signal92.960777
Spike_AFFX-r2-Bs-thr_avg-signal363.418457
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal946.535583
Spike_AFFX-r2-Bs-phe_5_signal166.226563
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1523.136353
RawQ1.972600
Spike_AFFX-r2-Bs-lys_5_signal96.331924
Signal(A)4.297828
%A37.409031
Signal(All)154.655548
Corner+Avg:100,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal414.433258
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal173.157578
Spike_AFFX-r2-Ec-bioD_avg-signal1234.835938
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.530468
Spike_AFFX-r2-Bs-lys_avg-signal82.532906
Spike_AFFX-r2-P1-cre_avg-signal4631.673828
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.060500
Spike_AFFX-r2-Bs-thr_3_signal601.169678
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-signal159.081650
Spike_AFFX-r2-Bs-dap_3_signal735.242188
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.609170
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal406.491394
#M470
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal105.847855
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.019538
Spike_AFFX-r2-Bs-thr_M_signal363.996094
Signal(P)252.298523
Spike_AFFX-r2-Bs-phe_3-5-ratio1.041696
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5777,Count:9
Spike_AFFX-r2-P1-cre_5_signal4304.214355
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8533
Signal(M)16.029516
BackgroundAvg:70.39,Std:0.41,Min:69.5,Max:71.9
Spike_AFFX-r2-Ec-bioC_avg-signal410.462341
Spike_AFFX-r2-Bs-dap_avg-signal524.383484
Spike_AFFX-r2-Bs-dap_3-5-ratio3.164413
Spike_AFFX-r2-Ec-bioB_5_signal96.556946
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.716042
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_548-5_stt3a-cglT_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 ("koiwa_548-5_stt3a-cglT_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_548-5_stt3a-cglT_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: cgl1-3, stt3a-2
Stock Code: N16368
Genetic Background: Col-0 (Columbia, N60000)
Age: 31 days old
Growth Conditions:
StratificationCold treatment for 2 days.
SterilisationWashed with 70% EtOH for 10 seconds and rinsed with distilled water for three times.
ProtocolSeeds were grown on 1/4 MS media supplemented with 0.5% sucrose and 0.8% agar in a growth chamber under long-day photoperiod (16-hr light, 8-hr darkness) at 24 ± 2°C for 10 days. Then, seedlings were transferred into soil and grown three more weeks in a growth chamber at 25 ± 2°C under long-day photoperiod at a light intensity of 40 µmol m-2s-1.
Soil ConstituentsSunGro Metromix 300: Contains 30-40% horticultural grade Vermiculite, Bark, Canadian Sphangum peat moss, horticultural grade Perlite, bark ash, Dolomitic limestone, and a wetting agent.
Plant Spacing5 in each pot
waterin every 2 days
Temperature23 °C average, 23 °C day, 23 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige and Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 40µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: shoot
Additional Organism Information:
Sample DescriptionRNA was extracted from shoots pooled from 5 plants
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

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

Labelling Protocol Information

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

Slide Information

Date Hybridised:

Array Design Information

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

Scanning Protocol Information

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

Image Analysis Information

Scaling Factor:1.524101
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-ratio1.102389
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.818883
Spike_AFFX-r2-Bs-dap_5_signal248.437027
NoiseAvg:1.54,Std:0.04,Min:1.4,Max:1.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal116.598541
#P12740
Spike_AFFX-r2-Bs-phe_M_signal138.422745
Corner-Avg:7403,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal298.833435
Spike_AFFX-r2-Ec-bioB_3_signal236.849167
Spike_AFFX-r2-Bs-lys_M_signal70.878784
Spike_AFFX-r2-P1-cre_3_signal12565.676758
Spike_AFFX-r2-Bs-lys_3-5-ratio1.534694
Spike_AFFX-r2-Bs-dap_M_signal488.055817
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.373028
Spike_AFFX-r2-Ec-bioB_avg-signal274.972382
Spike_AFFX-r2-Bs-thr_avg-signal306.591644
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal2989.507813
Spike_AFFX-r2-Bs-phe_5_signal136.003006
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal4242.368652
RawQ1.785481
Spike_AFFX-r2-Bs-lys_5_signal72.634407
Signal(A)6.500172
%A41.757999
Signal(All)170.275208
Corner+Avg:81,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal1161.460449
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal105.444504
Spike_AFFX-r2-Ec-bioD_avg-signal3615.938232
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P55.852695
Spike_AFFX-r2-Bs-lys_avg-signal84.994934
Spike_AFFX-r2-P1-cre_avg-signal11982.130859
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.389303
Spike_AFFX-r2-Bs-thr_3_signal509.888672
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-signal126.623413
Spike_AFFX-r2-Bs-dap_3_signal860.279114
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.419086
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal1040.003174
#M545
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal111.471619
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.116786
Spike_AFFX-r2-Bs-thr_M_signal293.287659
Signal(P)299.089355
Spike_AFFX-r2-Bs-phe_3-5-ratio0.775310
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5132,Count:9
Spike_AFFX-r2-P1-cre_5_signal11398.584961
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9525
Signal(M)21.403357
BackgroundAvg:42.09,Std:0.37,Min:40.9,Max:42.6
Spike_AFFX-r2-Ec-bioC_avg-signal1100.731812
Spike_AFFX-r2-Bs-dap_avg-signal532.257324
Spike_AFFX-r2-Bs-dap_3-5-ratio3.462765
Spike_AFFX-r2-Ec-bioB_5_signal289.234497
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.524101
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_548-6_stt3a-cglT_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_548-6_stt3a-cglT_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_548-6_stt3a-cglT_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: cgl1-3, stt3a-2
Stock Code: N16368
Genetic Background: Col-0 (Columbia, N60000)
Age: 31 days old
Growth Conditions:
StratificationCold treatment for 2 days.
SterilisationWashed with 70% EtOH for 10 seconds and rinsed with distilled water for three times.
ProtocolSeeds were grown on 1/4 MS media supplemented with 0.5% sucrose and 0.8% agar in a growth chamber under long-day photoperiod (16-hr light, 8-hr darkness) at 24 ± 2°C for 10 days. Then, seedlings were transferred into soil and grown three more weeks in a growth chamber at 25 ± 2°C under long-day photoperiod at a light intensity of 40 µmol m-2s-1.
Soil ConstituentsSunGro Metromix 300: Contains 30-40% horticultural grade Vermiculite, Bark, Canadian Sphangum peat moss, horticultural grade Perlite, bark ash, Dolomitic limestone, and a wetting agent.
Plant Spacing5 in each pot
waterin every 2 days
Temperature23 °C average, 23 °C day, 23 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige and Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 40µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: shoot
Additional Organism Information:
Sample DescriptionRNA was extracted from shoots pooled from 5 plants
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:0.575033
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-ratio1.204441
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.970752
Spike_AFFX-r2-Bs-dap_5_signal158.385834
NoiseAvg:2.20,Std:0.06,Min:2.0,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal63.246017
#P15822
Spike_AFFX-r2-Bs-phe_M_signal68.114784
Corner-Avg:12756,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal79.772507
Spike_AFFX-r2-Ec-bioB_3_signal63.798759
Spike_AFFX-r2-Bs-lys_M_signal25.788254
Spike_AFFX-r2-P1-cre_3_signal3406.778809
Spike_AFFX-r2-Bs-lys_3-5-ratio1.276484
Spike_AFFX-r2-Bs-dap_M_signal321.805115
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.002688
Spike_AFFX-r2-Ec-bioB_avg-signal69.764076
Spike_AFFX-r2-Bs-thr_avg-signal134.094543
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal522.169495
Spike_AFFX-r2-Bs-phe_5_signal98.769875
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal943.104614
RawQ2.021135
Spike_AFFX-r2-Bs-lys_5_signal40.088959
Signal(A)3.092819
%A29.215256
Signal(All)136.446274
Corner+Avg:120,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal242.762314
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal92.318901
Spike_AFFX-r2-Ec-bioD_avg-signal732.637085
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.364311
Spike_AFFX-r2-Bs-lys_avg-signal39.016708
Spike_AFFX-r2-P1-cre_avg-signal3117.646484
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.420430
Spike_AFFX-r2-Bs-thr_3_signal189.908066
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-signal86.401184
Spike_AFFX-r2-Bs-dap_3_signal429.159363
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.806127
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal181.345795
#M324
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal51.172909
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.338671
Spike_AFFX-r2-Bs-thr_M_signal149.129562
Signal(P)195.168472
Spike_AFFX-r2-Bs-phe_3-5-ratio0.934687
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11643,Count:9
Spike_AFFX-r2-P1-cre_5_signal2828.514160
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6664
Signal(M)11.646564
BackgroundAvg:72.40,Std:0.48,Min:70.9,Max:73.5
Spike_AFFX-r2-Ec-bioC_avg-signal212.054047
Spike_AFFX-r2-Bs-dap_avg-signal303.116791
Spike_AFFX-r2-Bs-dap_3-5-ratio2.709582
Spike_AFFX-r2-Ec-bioB_5_signal65.720985
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.575033
NF1.000000
HZ4
Tau0.015000

Slide: koiwa_548-7_stt3a-cglT_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 ("koiwa_548-7_stt3a-cglT_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_548-7_stt3a-cglT_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: cgl1-3, stt3a-2
Stock Code: N16368
Genetic Background: Col-0 (Columbia, N60000)
Age: 31 days old
Growth Conditions:
StratificationCold treatment for 2 days.
SterilisationWashed with 70% EtOH for 10 seconds and rinsed with distilled water for three times.
ProtocolSeeds were grown on 1/4 MS media supplemented with 0.5% sucrose and 0.8% agar in a growth chamber under long-day photoperiod (16-hr light, 8-hr darkness) at 24 ± 2°C for 10 days. Then, seedlings were transferred into soil and grown three more weeks in a growth chamber at 25 ± 2°C under long-day photoperiod at a light intensity of 40 µmol m-2s-1.
Soil ConstituentsSunGro Metromix 300: Contains 30-40% horticultural grade Vermiculite, Bark, Canadian Sphangum peat moss, horticultural grade Perlite, bark ash, Dolomitic limestone, and a wetting agent.
Plant Spacing5 in each pot
waterin every 2 days
Temperature23 °C average, 23 °C day, 23 °C night
Humidity50 % average, 50 % day, 50 % night
MediumMurashige and Skoog basal salt mixture
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 40µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.50
Tissue: shoot
Additional Organism Information:
Sample DescriptionRNA was extracted from shoots pooled from 5 plants
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:0.478136
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-ratio1.042833
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.905687
Spike_AFFX-r2-Bs-dap_5_signal115.795021
NoiseAvg:2.51,Std:0.06,Min:2.3,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal58.650898
#P15834
Spike_AFFX-r2-Bs-phe_M_signal58.482468
Corner-Avg:13246,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal80.113625
Spike_AFFX-r2-Ec-bioB_3_signal54.028484
Spike_AFFX-r2-Bs-lys_M_signal22.380785
Spike_AFFX-r2-P1-cre_3_signal2881.908936
Spike_AFFX-r2-Bs-lys_3-5-ratio1.510939
Spike_AFFX-r2-Bs-dap_M_signal284.844818
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.653075
Spike_AFFX-r2-Ec-bioB_avg-signal64.598930
Spike_AFFX-r2-Bs-thr_avg-signal114.482544
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal524.986389
Spike_AFFX-r2-Bs-phe_5_signal93.699615
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal882.479614
RawQ2.383898
Spike_AFFX-r2-Bs-lys_5_signal35.592331
Signal(A)2.874269
%A29.215256
Signal(All)136.613434
Corner+Avg:134,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal205.324707
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal84.526123
Spike_AFFX-r2-Ec-bioD_avg-signal703.733032
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.416924
Spike_AFFX-r2-Bs-lys_avg-signal37.250320
Spike_AFFX-r2-P1-cre_avg-signal2822.724121
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.367821
Spike_AFFX-r2-Bs-thr_3_signal155.605225
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal78.902733
Spike_AFFX-r2-Bs-dap_3_signal377.964447
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.680957
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal173.347427
#M312
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal53.777847
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.184469
Spike_AFFX-r2-Bs-thr_M_signal129.191498
Signal(P)195.364243
Spike_AFFX-r2-Bs-phe_3-5-ratio0.902097
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11684,Count:9
Spike_AFFX-r2-P1-cre_5_signal2763.539063
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6664
Signal(M)11.540915
BackgroundAvg:81.38,Std:0.85,Min:78.8,Max:83.2
Spike_AFFX-r2-Ec-bioC_avg-signal189.336060
Spike_AFFX-r2-Bs-dap_avg-signal259.534760
Spike_AFFX-r2-Bs-dap_3-5-ratio3.264082
Spike_AFFX-r2-Ec-bioB_5_signal59.654686
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.478136
NF1.000000
HZ4
Tau0.015000


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