NASC's International Affymetrix Service

AI logo

NASCArrays

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

Experiment: Xylella fastidiosa infection of Arabidopsis thaliana Tsu-1

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-582

The experiment compares Xylella fastidiosa (GFP labeled Temecula) inoculated Arabidopsis with mock inoculated tissue. Bacterial were mechanically inoculated into midrib of leaves. At 9dpi, midribs above the inoculation point were dissected out and frozen. Total RNA was isolated using Trizol, and hybridized to Affy ATH-1 arrays. Three biological replicate pairs of Xf and mock inoculated RNA were run.

About the Experimenter

Name: Elizabeth Rogers
Head of Lab Name: Elizabeth Rogers
Lab:
Address:USDA-ARS-SJVASC
9611 S. Riverbend Ave
Parlier, CA
Postcode: 93648
Country: United States
 

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: pathogenicity_design
Number of Slides:6
 
Experimental Parameters:
parameterinfect
Quality Control Measures Taken:
biological-replicates3
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Rogers: Xylella fastidiosa infection of Arabidopsis thaliana Tsu-1_genome

Slide: Rogers_Xylella-fastidiosa inoculated 3_SLD

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 ("Rogers_Xylella-fastidiosa inoculated 3_") 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: Rogers_Xylella-fastidiosa inoculated 3_
Organism: Arabidopsis thaliana
Alias: Tsu-1
Stock Code: CS22641
Age: 5 weeks
Growth Conditions:
Stratification3 days at 4oC in 0.1% agar
Protocolone plant per 2 1/4" pot of metromix 200, constant temp 22oC, 14 hr light/10 hr dark cycle, water as needed
Soil ConstituentsMetromix 200
waterbottom water as needed
Temperature22 °C average, 22 °C day, 22 °C night
Humidity80 % average, 80 % day, 80 % night
Medium
Lighting(Source: Cool white fluorescent. Wavelength: White)14 hour days, 10 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: leaf midrib from inoculated leaf
in vivo Treatment: plants were 4-4.5 weeks old at inoculation. Xylella fastidiosa (GFP Temecula from Steve Lindow) inoculation - 1 ul drop of bacteria OD600 = 0.2 in water on midrib at leaf-petiole junction and poked 4-5 times under drop with very small pin. harvest 9 dpi
Additional Organism Information:
Sample Descriptionfully mature plant, prior to bolting
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:0.846949
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-ratio1.336025
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.057629
Spike_AFFX-r2-Bs-dap_5_signal126.504051
NoiseAvg:7.22,Std:1.25,Min:4.9,Max:10.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal39.487385
#P12739
Spike_AFFX-r2-Bs-phe_M_signal105.868004
Corner-Avg:25094,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal288.347504
Spike_AFFX-r2-Ec-bioB_3_signal208.069748
Spike_AFFX-r2-Bs-lys_M_signal57.314129
Spike_AFFX-r2-P1-cre_3_signal8808.283203
Spike_AFFX-r2-Bs-lys_3-5-ratio2.177681
Spike_AFFX-r2-Bs-dap_M_signal429.964294
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.969048
Spike_AFFX-r2-Ec-bioB_avg-signal231.049866
Spike_AFFX-r2-Bs-thr_avg-signal138.041885
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1781.789185
Spike_AFFX-r2-Bs-phe_5_signal108.416702
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal2761.781738
RawQ3.276654
Spike_AFFX-r2-Bs-lys_5_signal62.372208
Signal(A)7.134305
%A41.977203
Signal(All)153.022659
Corner+Avg:188,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal465.716553
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal105.762657
Spike_AFFX-r2-Ec-bioD_avg-signal2271.785400
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P55.848312
Spike_AFFX-r2-Bs-lys_avg-signal85.171043
Spike_AFFX-r2-P1-cre_avg-signal7700.593750
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.174485
Spike_AFFX-r2-Bs-thr_3_signal235.702072
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-signal106.682457
Spike_AFFX-r2-Bs-dap_3_signal639.625427
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.550005
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal492.271118
#M496
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal135.826782
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.946057
Spike_AFFX-r2-Bs-thr_M_signal138.936172
Signal(P)267.716888
Spike_AFFX-r2-Bs-phe_3-5-ratio0.975520
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:19894,Count:9
Spike_AFFX-r2-P1-cre_5_signal6592.903809
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9575
Signal(M)23.569382
BackgroundAvg:82.01,Std:2.58,Min:75.6,Max:87.8
Spike_AFFX-r2-Ec-bioC_avg-signal478.993835
Spike_AFFX-r2-Bs-dap_avg-signal398.697906
Spike_AFFX-r2-Bs-dap_3-5-ratio5.056166
Spike_AFFX-r2-Ec-bioB_5_signal196.732346
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.846949
NF1.000000
HZ4
Tau0.015000

Slide: Rogers_Xylella-fastidiosa inoculated 2_SLD

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 ("Rogers_Xylella-fastidiosa inoculated 2_") 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: Rogers_Xylella-fastidiosa inoculated 2_
Organism: Arabidopsis thaliana
Alias: Tsu-1
Stock Code: CS22641
Age: 5 weeks
Growth Conditions:
Stratification3 days at 4oC in 0.1% agar
Protocolone plant per 2 1/4" pot of metromix 200, constant temp 22oC, 14 hr light/10 hr dark cycle, water as needed
Soil ConstituentsMetromix 200
waterbottom water as needed
Temperature22 °C average, 22 °C day, 22 °C night
Humidity80 % average, 80 % day, 80 % night
Medium
Lighting(Source: Cool white fluorescent. Wavelength: White)14 hour days, 10 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: leaf midrib from inoculated leaf
in vivo Treatment: plants were 4-4.5 weeks old at inoculation. Xylella fastidiosa (GFP Temecula from Steve Lindow) inoculation - 1 ul drop of bacteria OD600 = 0.2 in water on midrib at leaf-petiole junction and poked 4-5 times under drop with very small pin. harvest 9 dpi
Additional Organism Information:
Sample Descriptionfully mature plant, prior to bolting
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:0.928578
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-ratio1.425251
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.273688
Spike_AFFX-r2-Bs-dap_5_signal40.384682
NoiseAvg:4.45,Std:0.48,Min:3.7,Max:6.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.296171
#P11857
Spike_AFFX-r2-Bs-phe_M_signal55.100067
Corner-Avg:16899,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal401.455139
Spike_AFFX-r2-Ec-bioB_3_signal339.966064
Spike_AFFX-r2-Bs-lys_M_signal55.898510
Spike_AFFX-r2-P1-cre_3_signal12641.103516
Spike_AFFX-r2-Bs-lys_3-5-ratio1.164150
Spike_AFFX-r2-Bs-dap_M_signal267.569489
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.143003
Spike_AFFX-r2-Ec-bioB_avg-signal336.111938
Spike_AFFX-r2-Bs-thr_avg-signal78.350990
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal2703.835449
Spike_AFFX-r2-Bs-phe_5_signal69.521652
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal4029.093262
RawQ2.948021
Spike_AFFX-r2-Bs-lys_5_signal80.774620
Signal(A)7.978388
%A45.598423
Signal(All)167.829681
Corner+Avg:134,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal807.612122
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal91.389374
Spike_AFFX-r2-Ec-bioD_avg-signal3366.464355
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P51.981586
Spike_AFFX-r2-Bs-lys_avg-signal76.902306
Spike_AFFX-r2-P1-cre_avg-signal10755.245117
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.419991
Spike_AFFX-r2-Bs-thr_3_signal148.995956
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-signal72.003700
Spike_AFFX-r2-Bs-dap_3_signal553.430481
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.490140
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal954.788147
#M552
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal94.033768
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.845855
Spike_AFFX-r2-Bs-thr_M_signal69.760849
Signal(P)314.671844
Spike_AFFX-r2-Bs-phe_3-5-ratio1.314546
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14315,Count:9
Spike_AFFX-r2-P1-cre_5_signal8869.386719
Spike_AFFX-r2-Bs-phe_M_detectionP
#A10401
Signal(M)25.629990
BackgroundAvg:73.89,Std:1.60,Min:69.6,Max:77.7
Spike_AFFX-r2-Ec-bioC_avg-signal881.200134
Spike_AFFX-r2-Bs-dap_avg-signal287.128235
Spike_AFFX-r2-Bs-dap_3-5-ratio13.703970
Spike_AFFX-r2-Ec-bioB_5_signal266.914612
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.928578
NF1.000000
HZ4
Tau0.015000

Slide: Rogers_Xylella-fastidiosa inoculated 1_SLD

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 ("Rogers_Xylella-fastidiosa inoculated 1_") 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: Rogers_Xylella-fastidiosa inoculated 1_
Organism: Arabidopsis thaliana
Alias: Tsu-1
Stock Code: CS22641
Age: 5 weeks
Growth Conditions:
Stratification3 days at 4oC in 0.1% agar
Protocolone plant per 2 1/4" pot of metromix 200, constant temp 22oC, 14 hr light/10 hr dark cycle, water as needed
Soil ConstituentsMetromix 200
waterbottom water as needed
Temperature22 °C average, 22 °C day, 22 °C night
Humidity80 % average, 80 % day, 80 % night
Medium
Lighting(Source: Cool white fluorescent. Wavelength: White)14 hour days, 10 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: leaf midrib from inoculated leaf
in vivo Treatment: plants were 4-4.5 weeks old at inoculation. Xylella fastidiosa (GFP Temecula from Steve Lindow) inoculation - 1 ul drop of bacteria OD600 = 0.2 in water on midrib at leaf-petiole junction and poked 4-5 times under drop with very small pin. harvest 9 dpi
Additional Organism Information:
Sample Descriptionfully mature plant, prior to bolting
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:0.857065
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-ratio1.227304
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.998138
Spike_AFFX-r2-Bs-dap_5_signal31.233927
NoiseAvg:4.10,Std:0.55,Min:3.4,Max:6.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.716227
#P12455
Spike_AFFX-r2-Bs-phe_M_signal62.894817
Corner-Avg:17216,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal401.370239
Spike_AFFX-r2-Ec-bioB_3_signal317.956268
Spike_AFFX-r2-Bs-lys_M_signal52.316189
Spike_AFFX-r2-P1-cre_3_signal11521.965820
Spike_AFFX-r2-Bs-lys_3-5-ratio1.634251
Spike_AFFX-r2-Bs-dap_M_signal182.005203
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio19.302521
Spike_AFFX-r2-Ec-bioB_avg-signal345.958710
Spike_AFFX-r2-Bs-thr_avg-signal81.195328
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal2551.108154
Spike_AFFX-r2-Bs-phe_5_signal54.998268
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal4005.197266
RawQ2.993773
Spike_AFFX-r2-Bs-lys_5_signal59.612442
Signal(A)6.132830
%A43.314335
Signal(All)160.939835
Corner+Avg:135,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal804.963745
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal97.918022
Spike_AFFX-r2-Ec-bioD_avg-signal3278.152832
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P54.603245
Spike_AFFX-r2-Bs-lys_avg-signal69.783432
Spike_AFFX-r2-P1-cre_avg-signal10454.999023
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.082420
Spike_AFFX-r2-Bs-thr_3_signal168.245148
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-signal71.937035
Spike_AFFX-r2-Bs-dap_3_signal525.473450
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.569983
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal844.047546
#M475
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal97.421661
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.953695
Spike_AFFX-r2-Bs-thr_M_signal66.624611
Signal(P)289.043396
Spike_AFFX-r2-Bs-phe_3-5-ratio1.780384
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11791,Count:9
Spike_AFFX-r2-P1-cre_5_signal9388.032227
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9880
Signal(M)21.915653
BackgroundAvg:78.44,Std:1.39,Min:74.3,Max:81.0
Spike_AFFX-r2-Ec-bioC_avg-signal824.505615
Spike_AFFX-r2-Bs-dap_avg-signal246.237534
Spike_AFFX-r2-Bs-dap_3-5-ratio16.823803
Spike_AFFX-r2-Ec-bioB_5_signal318.549530
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.857065
NF1.000000
HZ4
Tau0.015000

Slide: Rogers_mock-inoculated 3_SLD

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 ("Rogers_mock-inoculated 3_") 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: Rogers_mock-inoculated 3_
Organism: Arabidopsis thaliana
Alias: Tsu-1
Stock Code: CS22641
Age: 5 weeks
Growth Conditions:
Stratification3 days at 4oC in 0.1% agar
Protocolone plant per 2 1/4" pot of metromix 200, constant temp 22oC, 14 hr light/10 hr dark cycle, water as needed
Soil ConstituentsMetromix 200
waterbottom water as needed
Temperature22 °C average, 22 °C day, 22 °C night
Humidity80 % average, 80 % day, 80 % night
Medium
Lighting(Source: Cool white fluorescent. Wavelength: White)14 hour days, 10 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: leaf midrib
in vivo Treatment: plants were 4-4.5 weeks old at inoculation. mock inoculation - 1 ul drop of water on midrib at leaf-petiole junction and poked 4-5 times under drop with very small pin. harvest 9 dpi
Additional Organism Information:
Sample Descriptionfully mature plant, prior to bolting
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:1.218563
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-ratio1.497911
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.831533
Spike_AFFX-r2-Bs-dap_5_signal135.099136
NoiseAvg:6.58,Std:0.93,Min:4.1,Max:9.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal42.008865
#P11756
Spike_AFFX-r2-Bs-phe_M_signal133.100632
Corner-Avg:24996,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal371.794586
Spike_AFFX-r2-Ec-bioB_3_signal246.295624
Spike_AFFX-r2-Bs-lys_M_signal66.182945
Spike_AFFX-r2-P1-cre_3_signal12412.013672
Spike_AFFX-r2-Bs-lys_3-5-ratio1.689726
Spike_AFFX-r2-Bs-dap_M_signal431.348694
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.491300
Spike_AFFX-r2-Ec-bioB_avg-signal304.761566
Spike_AFFX-r2-Bs-thr_avg-signal142.211441
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal2395.960449
Spike_AFFX-r2-Bs-phe_5_signal115.674385
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal4104.856445
RawQ3.344338
Spike_AFFX-r2-Bs-lys_5_signal59.431072
Signal(A)10.451421
%A46.032440
Signal(All)158.645340
Corner+Avg:192,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal666.223877
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal129.257645
Spike_AFFX-r2-Ec-bioD_avg-signal3250.408447
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P51.538799
Spike_AFFX-r2-Bs-lys_avg-signal75.345421
Spike_AFFX-r2-P1-cre_avg-signal10349.115234
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.428759
Spike_AFFX-r2-Bs-thr_3_signal230.683258
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-signal126.010887
Spike_AFFX-r2-Bs-dap_3_signal765.546204
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.713241
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal740.730042
#M554
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal100.422249
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.899415
Spike_AFFX-r2-Bs-thr_M_signal153.942245
Signal(P)296.807159
Spike_AFFX-r2-Bs-phe_3-5-ratio1.117427
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:20512,Count:9
Spike_AFFX-r2-P1-cre_5_signal8286.217773
Spike_AFFX-r2-Bs-phe_M_detectionP
#A10500
Signal(M)35.551170
BackgroundAvg:82.91,Std:2.11,Min:78.0,Max:87.3
Spike_AFFX-r2-Ec-bioC_avg-signal703.476929
Spike_AFFX-r2-Bs-dap_avg-signal443.998016
Spike_AFFX-r2-Bs-dap_3-5-ratio5.666552
Spike_AFFX-r2-Ec-bioB_5_signal296.194489
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.218563
NF1.000000
HZ4
Tau0.015000

Slide: Rogers_mock-inoculated 2_SLD

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 ("Rogers_mock-inoculated 2_") 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: Rogers_mock-inoculated 2_
Organism: Arabidopsis thaliana
Alias: Tsu-1
Stock Code: CS22641
Age: 5 weeks
Growth Conditions:
Stratification3 days at 4oC in 0.1% agar
Protocolone plant per 2 1/4" pot of metromix 200, constant temp 22oC, 14 hr light/10 hr dark cycle, water as needed
Soil ConstituentsMetromix 200
waterbottom water as needed
Temperature22 °C average, 22 °C day, 22 °C night
Humidity80 % average, 80 % day, 80 % night
Medium
Lighting(Source: Cool white fluorescent. Wavelength: White)14 hour days, 10 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: leaf midrib
in vivo Treatment: plants were 4-4.5 weeks old at inoculation. mock inoculation - 1 ul drop of water on midrib at leaf-petiole junction and poked 4-5 times under drop with very small pin. harvest 9 dpi
Additional Organism Information:
Sample Descriptionfully mature plant, prior to bolting
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:0.900649
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-ratio1.312963
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.217660
Spike_AFFX-r2-Bs-dap_5_signal43.894840
NoiseAvg:6.04,Std:0.53,Min:4.4,Max:7.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.030731
#P12197
Spike_AFFX-r2-Bs-phe_M_signal36.221874
Corner-Avg:16621,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal405.803284
Spike_AFFX-r2-Ec-bioB_3_signal323.491638
Spike_AFFX-r2-Bs-lys_M_signal77.252808
Spike_AFFX-r2-P1-cre_3_signal11853.479492
Spike_AFFX-r2-Bs-lys_3-5-ratio1.922500
Spike_AFFX-r2-Bs-dap_M_signal304.761627
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio17.769077
Spike_AFFX-r2-Ec-bioB_avg-signal331.653900
Spike_AFFX-r2-Bs-thr_avg-signal102.256172
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal2602.537598
Spike_AFFX-r2-Bs-phe_5_signal41.336430
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal4242.360840
RawQ2.929203
Spike_AFFX-r2-Bs-lys_5_signal73.066582
Signal(A)6.877575
%A44.256905
Signal(All)163.693588
Corner+Avg:134,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal830.605225
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal94.471313
Spike_AFFX-r2-Ec-bioD_avg-signal3422.449219
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P53.472160
Spike_AFFX-r2-Bs-lys_avg-signal96.929962
Spike_AFFX-r2-P1-cre_avg-signal10440.759766
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.270934
Spike_AFFX-r2-Bs-thr_3_signal213.774994
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-signal57.343204
Spike_AFFX-r2-Bs-dap_3_signal747.174561
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.630086
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal827.523071
#M518
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal140.470505
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.003725
Spike_AFFX-r2-Bs-thr_M_signal80.962799
Signal(P)299.370117
Spike_AFFX-r2-Bs-phe_3-5-ratio2.285425
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11986,Count:9
Spike_AFFX-r2-P1-cre_5_signal9028.039063
Spike_AFFX-r2-Bs-phe_M_detectionP
#A10095
Signal(M)25.105310
BackgroundAvg:74.30,Std:1.11,Min:69.6,Max:76.3
Spike_AFFX-r2-Ec-bioC_avg-signal829.064148
Spike_AFFX-r2-Bs-dap_avg-signal365.277008
Spike_AFFX-r2-Bs-dap_3-5-ratio17.021923
Spike_AFFX-r2-Ec-bioB_5_signal265.666718
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.900649
NF1.000000
HZ4
Tau0.015000

Slide: Rogers_mock-inoculated 1_SLD

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 ("Rogers_mock-inoculated 1_") 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: Rogers_mock-inoculated 1_
Organism: Arabidopsis thaliana
Alias: Tsu-1
Stock Code: CS22641
Age: 5 weeks
Growth Conditions:
Stratification3 days at 4oC in 0.1% agar
Protocolone plant per 2 1/4" pot of metromix 200, constant temp 22oC, 14 hr light/10 hr dark cycle, water as needed
Soil ConstituentsMetromix 200
waterbottom water as needed
Temperature22 °C average, 22 °C day, 22 °C night
Humidity80 % average, 80 % day, 80 % night
Medium
Lighting(Source: Cool white fluorescent. Wavelength: White)14 hour days, 10 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: leaf midrib
in vivo Treatment: plants were 4-4.5 weeks old at inoculation. mock inoculation - 1 ul drop of water on midrib at leaf-petiole junction and poked 4-5 times under drop with very small pin. harvest 9 dpi
Additional Organism Information:
Sample Descriptionfully mature plant, prior to bolting
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:1.154727
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-ratio1.199003
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.133814
Spike_AFFX-r2-Bs-dap_5_signal18.849195
NoiseAvg:5.62,Std:0.96,Min:4.0,Max:8.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.343750
#P12125
Spike_AFFX-r2-Bs-phe_M_signal27.601831
Corner-Avg:15429,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal361.812927
Spike_AFFX-r2-Ec-bioB_3_signal299.499023
Spike_AFFX-r2-Bs-lys_M_signal72.965622
Spike_AFFX-r2-P1-cre_3_signal10597.123047
Spike_AFFX-r2-Bs-lys_3-5-ratio1.575723
Spike_AFFX-r2-Bs-dap_M_signal141.764420
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio15.839518
Spike_AFFX-r2-Ec-bioB_avg-signal308.487885
Spike_AFFX-r2-Bs-thr_avg-signal77.026482
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal2117.721924
Spike_AFFX-r2-Bs-phe_5_signal33.798176
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal3001.169434
RawQ3.140014
Spike_AFFX-r2-Bs-lys_5_signal52.286163
Signal(A)9.107634
%A44.506794
Signal(All)154.460419
Corner+Avg:128,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal702.937195
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal70.657288
Spike_AFFX-r2-Ec-bioD_avg-signal2559.445801
Spike_AFFX-r2-Bs-dap_5_detectionM
Spike_AFFX-r2-Bs-phe_5_detectionP
%P53.156509
Spike_AFFX-r2-Bs-lys_avg-signal69.213440
Spike_AFFX-r2-P1-cre_avg-signal9717.701172
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.336694
Spike_AFFX-r2-Bs-thr_3_signal163.840012
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-signal44.019100
Spike_AFFX-r2-Bs-dap_3_signal427.928131
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.417169
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal669.946838
#M533
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal82.388535
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.049243
Spike_AFFX-r2-Bs-thr_M_signal56.895687
Signal(P)281.633270
Spike_AFFX-r2-Bs-phe_3-5-ratio2.090565
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12295,Count:9
Spike_AFFX-r2-P1-cre_5_signal8838.280273
Spike_AFFX-r2-Bs-phe_M_detectionP
#A10152
Signal(M)29.977140
BackgroundAvg:76.92,Std:4.06,Min:62.2,Max:84.8
Spike_AFFX-r2-Ec-bioC_avg-signal686.442017
Spike_AFFX-r2-Bs-dap_avg-signal196.180588
Spike_AFFX-r2-Bs-dap_3-5-ratio22.702726
Spike_AFFX-r2-Ec-bioB_5_signal264.151733
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.154727
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team