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Experiment: Escherichia coli O157:H7 Induces Stronger Plant Immunity than Salmonella enterica Typhimurium SL1344

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-674

There have been increased concerns of leafy vegetable contamination by human pathogens and food safety due to outbreaks associated with consumption of fresh produce. In this study, we assessed defense responses induced by the fully pathogenic bacteria Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium SL1344 in both Arabidopsis thaliana. Unlike SL1344, O157:H7 induces strong plant immunity at both pre-invasion and post-invasion steps of infection. For instance, O157:H7 triggers stomatal closure even under high relative humidity (RH); an environmental condition that generally weakens plant defenses against bacteria in the field and laboratory conditions. SL1344 instead induces a transient stomatal immunity. We also observed that O157:H7 modulates more components of innate immunity, i.e. genes and signaling pathways, as compared to SL1344. These results suggest that plants may recognize and respond to some human pathogens more effectively than others. Furthermore, stomatal immunity can diminish the penetration of human pathogens through the leaf epidermis resulting in low bacterial titers in the plant apoplast, which suggest that additional control measures can be employed to prevent food contamination. The understanding of how plant responses can diminish bacterial contamination is paramount in preventing outbreaks and improving the safety of food's supplies.

About the Experimenter

Name: Shweta Panchal
Head of Lab Name:Dr. Maeli Melotto
Lab:
Address:501 S. Nedderman Dr
Box 19498
Arlington, TX
Postcode: 76019
Country: USA
 

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: infect
Number of Slides:6
 
Experimental Parameters:
parameterinfect
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Panchal: Escherichia coli O157:H7 Induces Stronger Plant Immunity than Salmonella enterica Typhimurium SL1344

Slide: Panchal_674-6_Mock_7h_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 ("Panchal_674-6_Mock_7h_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: Panchal_674-6_Mock_7h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: N60000
Age: 4-5 weeks after germination
Growth Conditions:
Growth protocolArabidopsis thaliana (L. Heyhn.) seeds were sown in a 1:1:1 v:v:v mixture of growing medium (Redi-earth plug and seedling mix, Sun Gro), fine vermiculite, and perlite and grown in a controlled environmental chambers equipped with humidity control (Percival H2X Two Atomizer Humidifiers) at 22oC, 60±5% relative humidity, and a 12-h photoperiod under light intensity of 100 ìmol.m-2.s-1. For all experiments, four- to five-week old plants were used. The ecotype Columbia (Col-0, ABRC stock CS60000) was used as wild type plant.
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:0.593227
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-ratio2.186020
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.084483
Spike_AFFX-r2-Bs-dap_5_signal5.343101
NoiseAvg:2.04,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_signal14.234856
#P16990
Spike_AFFX-r2-Bs-phe_M_signal7.010161
Corner-Avg:8068,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal119.644615
Spike_AFFX-r2-Ec-bioB_3_signal88.822433
Spike_AFFX-r2-Bs-lys_M_signal6.228564
Spike_AFFX-r2-P1-cre_3_signal3906.857910
Spike_AFFX-r2-Bs-lys_3-5-ratio1.366291
Spike_AFFX-r2-Bs-dap_M_signal6.095106
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.217867
Spike_AFFX-r2-Ec-bioB_avg-signal96.790016
Spike_AFFX-r2-Bs-thr_avg-signal8.567299
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal794.774719
Spike_AFFX-r2-Bs-phe_5_signal3.889599
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1253.629883
RawQ2.219671
Spike_AFFX-r2-Bs-lys_5_signal5.422669
Signal(A)7.804776
%A21.665936
Signal(All)129.882843
Corner+Avg:95,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal337.077667
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal4.284163
Spike_AFFX-r2-Ec-bioD_avg-signal1024.202271
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P74.484879
Spike_AFFX-r2-Bs-lys_avg-signal6.353392
Spike_AFFX-r2-P1-cre_avg-signal2847.029785
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.849189
Spike_AFFX-r2-Bs-thr_3_signal3.101309
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-signal5.061308
Spike_AFFX-r2-Bs-dap_3_signal4.473022
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.577340
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal301.029419
#M878
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal7.408942
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.119750
Spike_AFFX-r2-Bs-thr_M_signal8.365732
Signal(P)171.293930
Spike_AFFX-r2-Bs-phe_3-5-ratio1.101441
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:5756,Count:9
Spike_AFFX-r2-P1-cre_5_signal1787.201660
Spike_AFFX-r2-Bs-phe_M_detectionM
#A4942
Signal(M)15.686278
BackgroundAvg:76.01,Std:0.47,Min:74.6,Max:77.0
Spike_AFFX-r2-Ec-bioC_avg-signal319.053528
Spike_AFFX-r2-Bs-dap_avg-signal5.303743
Spike_AFFX-r2-Bs-dap_3-5-ratio0.837158
Spike_AFFX-r2-Ec-bioB_5_signal81.903000
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.593227
NF1.000000
HZ4
Tau0.015000

Slide: Panchal_674-5_Mock_7h_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 ("Panchal_674-5_Mock_7h_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: Panchal_674-5_Mock_7h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: N60000
Age: 4-5 weeks after germination
Growth Conditions:
Growth protocolArabidopsis thaliana (L. Heyhn.) seeds were sown in a 1:1:1 v:v:v mixture of growing medium (Redi-earth plug and seedling mix, Sun Gro), fine vermiculite, and perlite and grown in a controlled environmental chambers equipped with humidity control (Percival H2X Two Atomizer Humidifiers) at 22oC, 60±5% relative humidity, and a 12-h photoperiod under light intensity of 100 ìmol.m-2.s-1. For all experiments, four- to five-week old plants were used. The ecotype Columbia (Col-0, ABRC stock CS60000) was used as wild type plant.
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:0.905957
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-ratio3.731430
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.953966
Spike_AFFX-r2-Bs-dap_5_signal5.196227
NoiseAvg:2.01,Std:0.09,Min:1.8,Max:2.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal20.693005
#P16142
Spike_AFFX-r2-Bs-phe_M_signal9.024882
Corner-Avg:7424,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal58.212753
Spike_AFFX-r2-Ec-bioB_3_signal80.757286
Spike_AFFX-r2-Bs-lys_M_signal11.268897
Spike_AFFX-r2-P1-cre_3_signal4342.625488
Spike_AFFX-r2-Bs-lys_3-5-ratio1.068983
Spike_AFFX-r2-Bs-dap_M_signal15.619315
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.547313
Spike_AFFX-r2-Ec-bioB_avg-signal74.541435
Spike_AFFX-r2-Bs-thr_avg-signal14.712865
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal543.057556
Spike_AFFX-r2-Bs-phe_5_signal9.618468
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1296.098267
RawQ2.331819
Spike_AFFX-r2-Bs-lys_5_signal8.659363
Signal(A)10.943847
%A25.098640
Signal(All)131.481537
Corner+Avg:106,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal236.800095
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal10.650769
Spike_AFFX-r2-Ec-bioD_avg-signal919.577881
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P70.767204
Spike_AFFX-r2-Bs-lys_avg-signal9.728323
Spike_AFFX-r2-P1-cre_avg-signal2753.210938
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M4.134151
Spike_AFFX-r2-Bs-thr_3_signal11.325550
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-signal9.764707
Spike_AFFX-r2-Bs-dap_3_signal4.313848
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.386668
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal292.718903
#M943
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal9.256709
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.808968
Spike_AFFX-r2-Bs-thr_M_signal12.120042
Signal(P)180.608337
Spike_AFFX-r2-Bs-phe_3-5-ratio1.107325
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:3156,Count:9
Spike_AFFX-r2-P1-cre_5_signal1163.796509
Spike_AFFX-r2-Bs-phe_M_detectionP
#A5725
Signal(M)22.333698
BackgroundAvg:73.74,Std:0.68,Min:71.7,Max:75.2
Spike_AFFX-r2-Ec-bioC_avg-signal264.759491
Spike_AFFX-r2-Bs-dap_avg-signal8.376463
Spike_AFFX-r2-Bs-dap_3-5-ratio0.830189
Spike_AFFX-r2-Ec-bioB_5_signal84.654266
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.905957
NF1.000000
HZ4
Tau0.015000

Slide: Panchal_674-4_Mock_7h_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 ("Panchal_674-4_Mock_7h_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: Panchal_674-4_Mock_7h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: N60000
Age: 4-5 weeks after germination
Growth Conditions:
Growth protocolArabidopsis thaliana (L. Heyhn.) seeds were sown in a 1:1:1 v:v:v mixture of growing medium (Redi-earth plug and seedling mix, Sun Gro), fine vermiculite, and perlite and grown in a controlled environmental chambers equipped with humidity control (Percival H2X Two Atomizer Humidifiers) at 22oC, 60±5% relative humidity, and a 12-h photoperiod under light intensity of 100 ìmol.m-2.s-1. For all experiments, four- to five-week old plants were used. The ecotype Columbia (Col-0, ABRC stock CS60000) was used as wild type plant.
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:0.541367
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-ratio1.347512
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.138456
Spike_AFFX-r2-Bs-dap_5_signal2.210014
NoiseAvg:2.14,Std:0.09,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_signal8.575417
#P16943
Spike_AFFX-r2-Bs-phe_M_signal2.952178
Corner-Avg:7711,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal83.974518
Spike_AFFX-r2-Ec-bioB_3_signal73.447739
Spike_AFFX-r2-Bs-lys_M_signal6.356452
Spike_AFFX-r2-P1-cre_3_signal2991.960938
Spike_AFFX-r2-Bs-lys_3-5-ratio1.083363
Spike_AFFX-r2-Bs-dap_M_signal5.496412
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.097862
Spike_AFFX-r2-Ec-bioB_avg-signal73.979156
Spike_AFFX-r2-Bs-thr_avg-signal4.493680
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal688.209534
Spike_AFFX-r2-Bs-phe_5_signal0.201387
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal995.210693
RawQ2.304873
Spike_AFFX-r2-Bs-lys_5_signal2.631049
Signal(A)7.536111
%A22.196405
Signal(All)124.896690
Corner+Avg:87,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal243.907883
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal6.887977
Spike_AFFX-r2-Ec-bioD_avg-signal841.710083
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P74.278824
Spike_AFFX-r2-Bs-lys_avg-signal3.945961
Spike_AFFX-r2-P1-cre_avg-signal2606.160400
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.524770
Spike_AFFX-r2-Bs-thr_3_signal0.839205
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-signal3.347180
Spike_AFFX-r2-Bs-dap_3_signal4.592453
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.446087
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal192.755386
#M804
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal2.850381
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.265375
Spike_AFFX-r2-Bs-thr_M_signal4.066418
Signal(P)165.190247
Spike_AFFX-r2-Bs-phe_3-5-ratio6.887977
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:4758,Count:9
Spike_AFFX-r2-P1-cre_5_signal2220.359863
Spike_AFFX-r2-Bs-phe_M_detectionA
#A5063
Signal(M)14.825693
BackgroundAvg:77.09,Std:0.50,Min:75.3,Max:78.4
Spike_AFFX-r2-Ec-bioC_avg-signal218.331635
Spike_AFFX-r2-Bs-dap_avg-signal4.099627
Spike_AFFX-r2-Bs-dap_3-5-ratio2.078019
Spike_AFFX-r2-Ec-bioB_5_signal64.515221
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.541367
NF1.000000
HZ4
Tau0.015000

Slide: Panchal_674-3_0e7-SL1344_7h_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 ("Panchal_674-3_0e7-SL1344_7h_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: Panchal_674-3_0e7-SL1344_7h_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: N60000
Age: 4-5 weeks after germination
Growth Conditions:
Growth protocolArabidopsis thaliana (L. Heyhn.) seeds were sown in a 1:1:1 v:v:v mixture of growing medium (Redi-earth plug and seedling mix, Sun Gro), fine vermiculite, and perlite and grown in a controlled environmental chambers equipped with humidity control (Percival H2X Two Atomizer Humidifiers) at 22oC, 60±5% relative humidity, and a 12-h photoperiod under light intensity of 100 ìmol.m-2.s-1. For all experiments, four- to five-week old plants were used. The ecotype Columbia (Col-0, ABRC stock CS60000) was used as wild type plant.
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:0.887298
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-ratio1.306248
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.279610
Spike_AFFX-r2-Bs-dap_5_signal6.246535
NoiseAvg:1.83,Std:0.09,Min:1.6,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_signal16.395952
#P15815
Spike_AFFX-r2-Bs-phe_M_signal12.308995
Corner-Avg:7770,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal149.873901
Spike_AFFX-r2-Ec-bioB_3_signal108.463013
Spike_AFFX-r2-Bs-lys_M_signal7.955918
Spike_AFFX-r2-P1-cre_3_signal5057.299316
Spike_AFFX-r2-Bs-lys_3-5-ratio0.666497
Spike_AFFX-r2-Bs-dap_M_signal3.033148
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.264084
Spike_AFFX-r2-Ec-bioB_avg-signal114.366486
Spike_AFFX-r2-Bs-thr_avg-signal8.284470
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal1042.298462
Spike_AFFX-r2-Bs-phe_5_signal0.444565
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1720.643555
RawQ2.204511
Spike_AFFX-r2-Bs-lys_5_signal6.994565
Signal(A)8.788791
%A27.115301
Signal(All)133.293549
Corner+Avg:86,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal371.694214
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal4.468462
Spike_AFFX-r2-Ec-bioD_avg-signal1381.470947
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P69.333626
Spike_AFFX-r2-Bs-lys_avg-signal6.537446
Spike_AFFX-r2-P1-cre_avg-signal4464.460449
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.551074
Spike_AFFX-r2-Bs-thr_3_signal4.329906
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-signal5.740674
Spike_AFFX-r2-Bs-dap_3_signal2.975509
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.650817
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal442.293518
#M810
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal4.661856
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.840379
Spike_AFFX-r2-Bs-thr_M_signal4.127550
Signal(P)187.860611
Spike_AFFX-r2-Bs-phe_3-5-ratio4.468462
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:3920,Count:9
Spike_AFFX-r2-P1-cre_5_signal3871.621338
Spike_AFFX-r2-Bs-phe_M_detectionA
#A6185
Signal(M)18.582211
BackgroundAvg:73.29,Std:0.71,Min:71.1,Max:74.7
Spike_AFFX-r2-Ec-bioC_avg-signal406.993866
Spike_AFFX-r2-Bs-dap_avg-signal4.085064
Spike_AFFX-r2-Bs-dap_3-5-ratio0.476345
Spike_AFFX-r2-Ec-bioB_5_signal84.762543
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.887298
NF1.000000
HZ4
Tau0.015000

Slide: Panchal_674-1_0e7-SL1344_7h_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 ("Panchal_674-1_0e7-SL1344_7h_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: Panchal_674-1_0e7-SL1344_7h_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: N60000
Age: 4-5 weeks after germination
Growth Conditions:
Growth protocolArabidopsis thaliana (L. Heyhn.) seeds were sown in a 1:1:1 v:v:v mixture of growing medium (Redi-earth plug and seedling mix, Sun Gro), fine vermiculite, and perlite and grown in a controlled environmental chambers equipped with humidity control (Percival H2X Two Atomizer Humidifiers) at 22oC, 60±5% relative humidity, and a 12-h photoperiod under light intensity of 100 ìmol.m-2.s-1. For all experiments, four- to five-week old plants were used. The ecotype Columbia (Col-0, ABRC stock CS60000) was used as wild type plant.
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:1.039372
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-ratio1.613121
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.510442
Spike_AFFX-r2-Bs-dap_5_signal4.559676
NoiseAvg:1.69,Std:0.06,Min:1.5,Max:1.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal8.861624
#P15855
Spike_AFFX-r2-Bs-phe_M_signal7.703848
Corner-Avg:5666,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal124.745201
Spike_AFFX-r2-Ec-bioB_3_signal120.463531
Spike_AFFX-r2-Bs-lys_M_signal6.882888
Spike_AFFX-r2-P1-cre_3_signal3515.277344
Spike_AFFX-r2-Bs-lys_3-5-ratio1.042967
Spike_AFFX-r2-Bs-dap_M_signal6.863678
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.374749
Spike_AFFX-r2-Ec-bioB_avg-signal108.320854
Spike_AFFX-r2-Bs-thr_avg-signal4.327035
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal648.751953
Spike_AFFX-r2-Bs-phe_5_signal0.296868
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1360.707275
RawQ2.091274
Spike_AFFX-r2-Bs-lys_5_signal5.011715
Signal(A)8.781651
%A26.808418
Signal(All)130.928802
Corner+Avg:65,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal373.257965
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal4.222200
Spike_AFFX-r2-Ec-bioD_avg-signal1004.729614
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P69.508987
Spike_AFFX-r2-Bs-lys_avg-signal5.707219
Spike_AFFX-r2-P1-cre_avg-signal2847.227539
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.682595
Spike_AFFX-r2-Bs-thr_3_signal3.320889
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-signal4.074305
Spike_AFFX-r2-Bs-dap_3_signal8.504497
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.097423
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal311.408478
#M840
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal5.227053
Spike_AFFX-r2-Bs-dap_M_detectionM
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.198612
Spike_AFFX-r2-Bs-thr_M_signal0.798594
Signal(P)184.021896
Spike_AFFX-r2-Bs-phe_3-5-ratio4.222200
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:3052,Count:9
Spike_AFFX-r2-P1-cre_5_signal2179.177490
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6115
Signal(M)17.998926
BackgroundAvg:72.17,Std:0.61,Min:70.7,Max:73.4
Spike_AFFX-r2-Ec-bioC_avg-signal342.333221
Spike_AFFX-r2-Bs-dap_avg-signal6.642617
Spike_AFFX-r2-Bs-dap_3-5-ratio1.865154
Spike_AFFX-r2-Ec-bioB_5_signal79.753815
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF1.039372
NF1.000000
HZ4
Tau0.015000

Slide: Panchal_674-2_0e7-SL1344_7h_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 ("Panchal_674-2_0e7-SL1344_7h_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: Panchal_674-2_0e7-SL1344_7h_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: N60000
Age: 4-5 weeks after germination
Growth Conditions:
Growth protocolArabidopsis thaliana (L. Heyhn.) seeds were sown in a 1:1:1 v:v:v mixture of growing medium (Redi-earth plug and seedling mix, Sun Gro), fine vermiculite, and perlite and grown in a controlled environmental chambers equipped with humidity control (Percival H2X Two Atomizer Humidifiers) at 22oC, 60±5% relative humidity, and a 12-h photoperiod under light intensity of 100 ìmol.m-2.s-1. For all experiments, four- to five-week old plants were used. The ecotype Columbia (Col-0, ABRC stock CS60000) was used as wild type plant.
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:0.617247
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-ratio1.388639
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.363299
Spike_AFFX-r2-Bs-dap_5_signal4.245580
NoiseAvg:1.89,Std:0.07,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_signal6.568781
#P15962
Spike_AFFX-r2-Bs-phe_M_signal3.053733
Corner-Avg:7118,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal106.567657
Spike_AFFX-r2-Ec-bioB_3_signal97.117401
Spike_AFFX-r2-Bs-lys_M_signal0.427260
Spike_AFFX-r2-P1-cre_3_signal3702.412842
Spike_AFFX-r2-Bs-lys_3-5-ratio4.659317
Spike_AFFX-r2-Bs-dap_M_signal1.803975
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio0.113551
Spike_AFFX-r2-Ec-bioB_avg-signal91.640694
Spike_AFFX-r2-Bs-thr_avg-signal4.626666
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionA
Spike_AFFX-r2-Ec-bioD_5_signal754.304932
Spike_AFFX-r2-Bs-phe_5_signal3.336083
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1121.358643
RawQ1.857330
Spike_AFFX-r2-Bs-lys_5_signal0.371130
Signal(A)6.545575
%A26.501534
Signal(All)130.549301
Corner+Avg:87,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal292.431458
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal3.056316
Spike_AFFX-r2-Ec-bioD_avg-signal937.831787
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P69.978081
Spike_AFFX-r2-Bs-lys_avg-signal1.819235
Spike_AFFX-r2-P1-cre_avg-signal3184.314453
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.520386
Spike_AFFX-r2-Bs-thr_3_signal0.745890
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-signal3.148711
Spike_AFFX-r2-Bs-dap_3_signal1.612676
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.486612
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal261.107788
#M803
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal4.659317
Spike_AFFX-r2-Bs-dap_M_detectionA
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.119964
Spike_AFFX-r2-Bs-thr_M_signal6.565325
Signal(P)183.417526
Spike_AFFX-r2-Bs-phe_3-5-ratio0.916139
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:5331,Count:9
Spike_AFFX-r2-P1-cre_5_signal2666.216309
Spike_AFFX-r2-Bs-phe_M_detectionA
#A6045
Signal(M)13.139530
BackgroundAvg:71.26,Std:0.40,Min:70.1,Max:72.1
Spike_AFFX-r2-Ec-bioC_avg-signal276.769623
Spike_AFFX-r2-Bs-dap_avg-signal2.554077
Spike_AFFX-r2-Bs-dap_3-5-ratio0.379848
Spike_AFFX-r2-Ec-bioB_5_signal71.237030
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.617247
NF1.000000
HZ4
Tau0.015000


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