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Experiment: N6-adenosine methylation deficient plant

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-612

The embryo leathal adenosine methylase (AT4G10760) tDNA knockout line SALK_074069 was partially complemented with its cDNA driven by the embryo specific ABI3 promoter. The partially complemented plants have reduced adenosine methylation and show pleiotropic phenotypes.Rosette leaves were harvested from 3-month-old plants maintained in growth camber under a 20 h photoperiod (23 degree C).

About the Experimenter

Name: silin zhong
Head of Lab Name: rupert fray
Lab:
Address:plant sciences
university of nottingham
Postcode: le12 5rd
Country: UK
 

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

About this Experiment

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

Slides in this Experiment

Hybridisation Set: zhong: N6-adenosine methylation deficient plant

Slide: Zhong_2-1_WT-rosette-leaf_Rep1_ATH1

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

Summary Information

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

  • Extract 1 ("Zhong_2-1_WT-rosette-leaf_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: Zhong_2-1_WT-rosette-leaf_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratification3 day in 4 degree C
ProtocolPlants were grown in 9 cm pots in growth camber. Photoperiod: 20 h light started at 22:00 (23 degree C) followed by 4 h night maintained at 20 degree C. Samples were harvested at 12:30 after 3 months.
Soil Constituentsnone
Temperature23 °C average, 23 °C day, 20 °C night
Humidity100 % average, 100 % day, 100 % night
Medium
Lighting20 hour days, 4 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: rosette leaf
Additional Organism Information:
Sample Description3-month-old wild-type (Col)
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:1.673768
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-ratio1.371445
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.322990
Spike_AFFX-r2-Bs-dap_5_signal0.688554
NoiseAvg:2.06,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_signal12.984593
#P12611
Spike_AFFX-r2-Bs-phe_M_signal2.973205
Corner-Avg:6133,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal125.707932
Spike_AFFX-r2-Ec-bioB_3_signal112.866188
Spike_AFFX-r2-Bs-lys_M_signal6.370967
Spike_AFFX-r2-P1-cre_3_signal6608.973145
Spike_AFFX-r2-Bs-lys_3-5-ratio1.448775
Spike_AFFX-r2-Bs-dap_M_signal2.324883
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.051228
Spike_AFFX-r2-Ec-bioB_avg-signal107.961853
Spike_AFFX-r2-Bs-thr_avg-signal6.903145
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal1098.261963
Spike_AFFX-r2-Bs-phe_5_signal0.615236
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1344.729980
RawQ2.213016
Spike_AFFX-r2-Bs-lys_5_signal0.310656
Signal(A)8.430113
%A42.626041
Signal(All)155.823257
Corner+Avg:55,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal322.277039
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal5.034258
Spike_AFFX-r2-Ec-bioD_avg-signal1221.495972
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P55.287155
Spike_AFFX-r2-Bs-lys_avg-signal2.710133
Spike_AFFX-r2-P1-cre_avg-signal5713.978516
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.086804
Spike_AFFX-r2-Bs-thr_3_signal0.665181
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal2.874233
Spike_AFFX-r2-Bs-dap_3_signal0.686443
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.224416
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal328.362213
#M476
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal1.448775
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.981468
Spike_AFFX-r2-Bs-thr_M_signal7.059662
Signal(P)274.220459
Spike_AFFX-r2-Bs-phe_3-5-ratio5.034258
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:5349,Count:9
Spike_AFFX-r2-P1-cre_5_signal4818.984375
Spike_AFFX-r2-Bs-phe_M_detectionA
#A9723
Signal(M)29.765324
BackgroundAvg:51.92,Std:0.22,Min:51.2,Max:52.6
Spike_AFFX-r2-Ec-bioC_avg-signal325.319641
Spike_AFFX-r2-Bs-dap_avg-signal1.233293
Spike_AFFX-r2-Bs-dap_3-5-ratio0.686443
Spike_AFFX-r2-Ec-bioB_5_signal85.311440
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.673768
NF1.000000
HZ4
Tau0.015000

Slide: Zhong_2-2_WT-rosette-leaf_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 ("Zhong_2-2_WT-rosette-leaf_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: Zhong_2-2_WT-rosette-leaf_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratification3 day in 4 degree C
ProtocolPlants were grown in 9 cm pots in growth camber. Photoperiod: 20 h light started at 22:00 (23 degree C) followed by 4 h night maintained at 20 degree C. Samples were harvested at 12:30 after 3 months.
Soil Constituentsnone
Temperature23 °C average, 23 °C day, 20 °C night
Humidity100 % average, 100 % day, 100 % night
Medium
Lighting20 hour days, 4 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: rosette leaf
Additional Organism Information:
Sample Description3-month-old wild-type (Col)
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:0.897617
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-ratio1.328458
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.272122
Spike_AFFX-r2-Bs-dap_5_signal2.796793
NoiseAvg:2.04,Std:0.06,Min:1.9,Max:2.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal2.761087
#P14005
Spike_AFFX-r2-Bs-phe_M_signal0.368355
Corner-Avg:7046,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal91.039665
Spike_AFFX-r2-Ec-bioB_3_signal77.274094
Spike_AFFX-r2-Bs-lys_M_signal3.312240
Spike_AFFX-r2-P1-cre_3_signal4718.445313
Spike_AFFX-r2-Bs-lys_3-5-ratio4.151917
Spike_AFFX-r2-Bs-dap_M_signal0.247091
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.279604
Spike_AFFX-r2-Ec-bioB_avg-signal76.352669
Spike_AFFX-r2-Bs-thr_avg-signal1.557240
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal752.239319
Spike_AFFX-r2-Bs-phe_5_signal1.015559
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal985.790283
RawQ2.181015
Spike_AFFX-r2-Bs-lys_5_signal1.790780
Signal(A)4.299387
%A37.018852
Signal(All)148.565842
Corner+Avg:69,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal220.176758
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal0.359035
Spike_AFFX-r2-Ec-bioD_avg-signal869.014771
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P61.398510
Spike_AFFX-r2-Bs-lys_avg-signal4.179397
Spike_AFFX-r2-P1-cre_avg-signal4135.132813
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.582639
Spike_AFFX-r2-Bs-thr_3_signal0.772011
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal0.580983
Spike_AFFX-r2-Bs-dap_3_signal1.456892
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.310474
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal219.481857
#M361
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal7.435170
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.003166
Spike_AFFX-r2-Bs-thr_M_signal1.138622
Signal(P)238.936462
Spike_AFFX-r2-Bs-phe_3-5-ratio0.353534
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:5651,Count:9
Spike_AFFX-r2-P1-cre_5_signal3551.820557
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8444
Signal(M)17.112745
BackgroundAvg:50.07,Std:0.58,Min:49.0,Max:51.5
Spike_AFFX-r2-Ec-bioC_avg-signal219.829315
Spike_AFFX-r2-Bs-dap_avg-signal1.500259
Spike_AFFX-r2-Bs-dap_3-5-ratio0.520915
Spike_AFFX-r2-Ec-bioB_5_signal60.744270
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.897617
NF1.000000
HZ4
Tau0.015000

Slide: Zhong_2-3_WT-rosette-leaf_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 ("Zhong_2-3_WT-rosette-leaf_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: Zhong_2-3_WT-rosette-leaf_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Growth Conditions:
Stratification3 day in 4 degree C
ProtocolPlants were grown in 9 cm pots in growth camber. Photoperiod: 20 h light started at 22:00 (23 degree C) followed by 4 h night maintained at 20 degree C. Samples were harvested at 12:30 after 3 months.
Soil Constituentsnone
Temperature23 °C average, 23 °C day, 20 °C night
Humidity100 % average, 100 % day, 100 % night
Medium
Lighting20 hour days, 4 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: rosette leaf
Additional Organism Information:
Sample Description3-month-old wild-type (Col)
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:0.841244
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-ratio1.320502
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.944933
Spike_AFFX-r2-Bs-dap_5_signal0.620148
NoiseAvg:2.29,Std:0.08,Min:2.1,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal4.586012
#P13859
Spike_AFFX-r2-Bs-phe_M_signal2.495226
Corner-Avg:6828,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal66.264748
Spike_AFFX-r2-Ec-bioB_3_signal61.442505
Spike_AFFX-r2-Bs-lys_M_signal9.284966
Spike_AFFX-r2-P1-cre_3_signal3833.589600
Spike_AFFX-r2-Bs-lys_3-5-ratio1.973776
Spike_AFFX-r2-Bs-dap_M_signal0.448776
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.058558
Spike_AFFX-r2-Ec-bioB_avg-signal64.243469
Spike_AFFX-r2-Bs-thr_avg-signal2.460945
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal522.751953
Spike_AFFX-r2-Bs-phe_5_signal0.686446
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal783.672607
RawQ2.246249
Spike_AFFX-r2-Bs-lys_5_signal3.900175
Signal(A)5.024649
%A37.527401
Signal(All)145.426346
Corner+Avg:65,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal231.232300
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal2.778859
Spike_AFFX-r2-Ec-bioD_avg-signal653.212280
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P60.758438
Spike_AFFX-r2-Bs-lys_avg-signal6.961071
Spike_AFFX-r2-P1-cre_avg-signal3368.359619
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.714160
Spike_AFFX-r2-Bs-thr_3_signal0.268546
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal1.986844
Spike_AFFX-r2-Bs-dap_3_signal0.415074
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.499129
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal206.423477
#M391
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal7.698071
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.120184
Spike_AFFX-r2-Bs-thr_M_signal2.528277
Signal(P)235.739029
Spike_AFFX-r2-Bs-phe_3-5-ratio2.778859
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:5267,Count:9
Spike_AFFX-r2-P1-cre_5_signal2903.129639
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8560
Signal(M)18.047770
BackgroundAvg:52.94,Std:0.66,Min:51.5,Max:54.2
Spike_AFFX-r2-Ec-bioC_avg-signal218.827881
Spike_AFFX-r2-Bs-dap_avg-signal0.494666
Spike_AFFX-r2-Bs-dap_3-5-ratio0.415074
Spike_AFFX-r2-Ec-bioB_5_signal65.023155
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.841244
NF1.000000
HZ4
Tau0.015000

Slide: Zhong_2-4_A6-rosette-leaf_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 ("Zhong_2-4_A6-rosette-leaf_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: Zhong_2-4_A6-rosette-leaf_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_074069 (AJ) (AN)
Stock Code: N574069
Genetic Background: Col-0 (Columbia, N60000)
Growth Conditions:
Stratification3 day in 4 degree C
ProtocolPlants were grown in 9 cm pots in growth camber. Photoperiod: 20 h light started at 22:00 (23 degree C) followed by 4 h night maintained at 20 degree C. Samples were harvested at 12:30 after 3 months.
Soil Constituentsnone
Temperature23 °C average, 23 °C day, 20 °C night
Humidity100 % average, 100 % day, 100 % night
Medium
Lighting20 hour days, 4 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: rosette leaf
Additional Organism Information:
Sample Description3-month-old partially complemented N574069
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:0.989263
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-ratio1.332488
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.330492
Spike_AFFX-r2-Bs-dap_5_signal0.474449
NoiseAvg:2.08,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_signal0.801293
#P13946
Spike_AFFX-r2-Bs-phe_M_signal1.064227
Corner-Avg:6906,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal88.621132
Spike_AFFX-r2-Ec-bioB_3_signal86.944969
Spike_AFFX-r2-Bs-lys_M_signal3.988308
Spike_AFFX-r2-P1-cre_3_signal5293.524902
Spike_AFFX-r2-Bs-lys_3-5-ratio1.869272
Spike_AFFX-r2-Bs-dap_M_signal1.491750
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.345371
Spike_AFFX-r2-Ec-bioB_avg-signal80.304688
Spike_AFFX-r2-Bs-thr_avg-signal0.749231
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal907.111938
Spike_AFFX-r2-Bs-phe_5_signal2.978969
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1077.209839
RawQ2.038978
Spike_AFFX-r2-Bs-lys_5_signal3.567723
Signal(A)4.956158
%A37.198597
Signal(All)151.925323
Corner+Avg:66,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal260.041992
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal6.468041
Spike_AFFX-r2-Ec-bioD_avg-signal992.160889
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P61.139851
Spike_AFFX-r2-Bs-lys_avg-signal4.741692
Spike_AFFX-r2-P1-cre_avg-signal4633.093750
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.661552
Spike_AFFX-r2-Bs-thr_3_signal0.345371
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal3.503746
Spike_AFFX-r2-Bs-dap_3_signal1.013316
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.187516
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal235.839264
#M379
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal6.669044
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.102624
Spike_AFFX-r2-Bs-thr_M_signal1.101028
Signal(P)244.931122
Spike_AFFX-r2-Bs-phe_3-5-ratio2.171235
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:5930,Count:9
Spike_AFFX-r2-P1-cre_5_signal3972.662109
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8485
Signal(M)19.932062
BackgroundAvg:49.41,Std:0.45,Min:48.5,Max:50.5
Spike_AFFX-r2-Ec-bioC_avg-signal247.940628
Spike_AFFX-r2-Bs-dap_avg-signal0.993171
Spike_AFFX-r2-Bs-dap_3-5-ratio1.013316
Spike_AFFX-r2-Ec-bioB_5_signal65.347969
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.989263
NF1.000000
HZ4
Tau0.015000

Slide: Zhong_2-5_A6-rosette-leaf_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 ("Zhong_2-5_A6-rosette-leaf_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: Zhong_2-5_A6-rosette-leaf_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_074069 (AJ) (AN)
Stock Code: N574069
Genetic Background: Col-0 (Columbia, N60000)
Growth Conditions:
Stratification3 day in 4 degree C
ProtocolPlants were grown in 9 cm pots in growth camber. Photoperiod: 20 h light started at 22:00 (23 degree C) followed by 4 h night maintained at 20 degree C. Samples were harvested at 12:30 after 3 months.
Soil Constituentsnone
Temperature23 °C average, 23 °C day, 20 °C night
Humidity100 % average, 100 % day, 100 % night
Medium
Lighting20 hour days, 4 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: rosette leaf
Additional Organism Information:
Sample Description3-month-old partially complemented N574069
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:0.969961
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-ratio1.290257
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.185506
Spike_AFFX-r2-Bs-dap_5_signal0.734667
NoiseAvg:2.11,Std:0.07,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_signal4.722519
#P14139
Spike_AFFX-r2-Bs-phe_M_signal7.002267
Corner-Avg:6556,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal88.519295
Spike_AFFX-r2-Ec-bioB_3_signal84.179695
Spike_AFFX-r2-Bs-lys_M_signal2.896409
Spike_AFFX-r2-P1-cre_3_signal4803.596191
Spike_AFFX-r2-Bs-lys_3-5-ratio4.104949
Spike_AFFX-r2-Bs-dap_M_signal2.738752
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.077975
Spike_AFFX-r2-Ec-bioB_avg-signal81.235451
Spike_AFFX-r2-Bs-thr_avg-signal1.934022
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal782.452881
Spike_AFFX-r2-Bs-phe_5_signal0.307529
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1088.403809
RawQ2.095397
Spike_AFFX-r2-Bs-lys_5_signal0.501924
Signal(A)5.290466
%A36.185883
Signal(All)151.335831
Corner+Avg:58,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal250.542404
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal3.550832
Spike_AFFX-r2-Ec-bioD_avg-signal935.428345
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P61.985970
Spike_AFFX-r2-Bs-lys_avg-signal2.501094
Spike_AFFX-r2-P1-cre_avg-signal4263.286133
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.828146
Spike_AFFX-r2-Bs-thr_3_signal0.368240
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal3.620209
Spike_AFFX-r2-Bs-dap_3_signal3.925445
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.391015
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal216.581238
#M417
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal4.104949
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.156806
Spike_AFFX-r2-Bs-thr_M_signal0.711307
Signal(P)240.461777
Spike_AFFX-r2-Bs-phe_3-5-ratio3.550832
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:5562,Count:9
Spike_AFFX-r2-P1-cre_5_signal3722.975830
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8254
Signal(M)20.176821
BackgroundAvg:51.46,Std:0.19,Min:50.7,Max:51.9
Spike_AFFX-r2-Ec-bioC_avg-signal233.561829
Spike_AFFX-r2-Bs-dap_avg-signal2.466288
Spike_AFFX-r2-Bs-dap_3-5-ratio3.925445
Spike_AFFX-r2-Ec-bioB_5_signal71.007370
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.969961
NF1.000000
HZ4
Tau0.015000

Slide: Zhong_2-6_A6-rosette-leaf_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 ("Zhong_2-6_A6-rosette-leaf_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: Zhong_2-6_A6-rosette-leaf_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_074069 (AJ) (AN)
Stock Code: N574069
Genetic Background: Col-0 (Columbia, N60000)
Growth Conditions:
Stratification3 day in 4 degree C
ProtocolPlants were grown in 9 cm pots in growth camber. Photoperiod: 20 h light started at 22:00 (23 degree C) followed by 4 h night maintained at 20 degree C. Samples were harvested at 12:30 after 3 months.
Soil Constituentsnone
Temperature23 °C average, 23 °C day, 20 °C night
Humidity100 % average, 100 % day, 100 % night
Medium
Lighting20 hour days, 4 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: rosette leaf
Additional Organism Information:
Sample Description3-month-old partially complemented N574069
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:1.380157
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-ratio1.319575
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.138959
Spike_AFFX-r2-Bs-dap_5_signal1.160143
NoiseAvg:1.96,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_signal11.846931
#P13456
Spike_AFFX-r2-Bs-phe_M_signal0.511829
Corner-Avg:6273,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal109.405632
Spike_AFFX-r2-Ec-bioB_3_signal98.583916
Spike_AFFX-r2-Bs-lys_M_signal3.751506
Spike_AFFX-r2-P1-cre_3_signal6336.052246
Spike_AFFX-r2-Bs-lys_3-5-ratio0.738960
Spike_AFFX-r2-Bs-dap_M_signal0.599306
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.054876
Spike_AFFX-r2-Ec-bioB_avg-signal98.181908
Spike_AFFX-r2-Bs-thr_avg-signal4.491238
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal973.907410
Spike_AFFX-r2-Bs-phe_5_signal0.491899
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1266.207520
RawQ1.989122
Spike_AFFX-r2-Bs-lys_5_signal3.457298
Signal(A)7.050067
%A39.017975
Signal(All)157.144485
Corner+Avg:54,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal419.749939
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal8.730900
Spike_AFFX-r2-Ec-bioD_avg-signal1120.057495
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P58.991669
Spike_AFFX-r2-Bs-lys_avg-signal3.254536
Spike_AFFX-r2-P1-cre_avg-signal5568.819336
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.990355
Spike_AFFX-r2-Bs-thr_3_signal0.650109
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal3.244876
Spike_AFFX-r2-Bs-dap_3_signal1.451607
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.300131
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal343.135254
#M454
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal2.554803
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.223278
Spike_AFFX-r2-Bs-thr_M_signal0.976675
Signal(P)260.863342
Spike_AFFX-r2-Bs-phe_3-5-ratio8.730900
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:4600,Count:9
Spike_AFFX-r2-P1-cre_5_signal4801.586914
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8900
Signal(M)25.425293
BackgroundAvg:47.97,Std:0.63,Min:46.3,Max:49.2
Spike_AFFX-r2-Ec-bioC_avg-signal381.442596
Spike_AFFX-r2-Bs-dap_avg-signal1.070352
Spike_AFFX-r2-Bs-dap_3-5-ratio1.251231
Spike_AFFX-r2-Ec-bioB_5_signal86.556175
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.380157
NF1.000000
HZ4
Tau0.015000


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