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Experiment: Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-76

Background:

Release of the caesium radioisotope 137Cs during weapons testing and industrial activity has contaminated thousands of hectares of agricultural land. Ingesting 137Cs has damaging and, sometimes, fatal effects. Most Cs enters the food chain through plants. The generation of _safe_ crops that exclude Cs and can be cultivated on contaminated land requires knowledge about the mechanisms for Cs uptake. Caesium is chemically similar to potassium (K) and might enter plants through K+ transporters in the plasma membrane of root cells.

To determine which transporters mediate Cs entry to plants, we have compared the accumulation of Cs and K by wildtype Arabidopsis with mutants lacking specific K+ transporters. Preliminary results showed that Cs concentration in the shoots of akt1-1, cngc1 and cngc4 (obtained from the Wisconsin T-DNA knockout facility) differed significantly from the Wassilewskija wildtype (Ws-2). A cursory investigation of their transcriptome, using the Affymetrix Arabidopsis 8K GeneChip, showed that the expression of several genes encoding K+ transporters differed between mutants and wildtype plants.

The aim of this GarNet project is to confirm the previous observations and to identify further genes that are differentially expressed in mutant and wildtype plants and which might impact on Cs accumulation.

Methods:

Arabidopsis mutants akt1-1 (N3762), cngc1 and cngc4 and their parental ecotype Wassilewskija -2 (N1601) will be sown on MS agar and transferred to hydroponics 21 days after germination. Seedlings will be grown for a further 7 days on full nutrient solution under continuous light in a Saxcil growth cabinet. RNA will be extracted from roots of mutant and parent (control) plants at the same growth stage and twelve complete-genome Affymetrix GeneChips (3 biological replicates of material from wildtype and 3 mutants) are requested to determine the differences in their transcriptome under comparable environmental conditions.

About the Experimenter

Name:Miss Corrina Hampton
Head of Lab Name:Dr Philip White
Lab:
Institute: Horticulture Research International
Address:Horticulture Research International
Wellesbourne
Warwick
Postcode: CV35 9EF
Country: UK
 
Telephone Number: 01789 470382
Fax Number: 01789 470552

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

About this Experiment

Experiment Type: genetic_modification_design
Number of Slides:12
 
Experimental Parameters:
parametergenetic_modification
Quality Control Measures Taken:
no-plants-pooled20-40
References:
 
Other Information:
ArrayExpress AccessionE-NASC-31

Slides in this Experiment

Hybridisation Set: Hampton_genome_Rep1

Slide: Hampton_1-1_ws2_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 ("Hampton_1-1_ws2_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: Hampton_1-1_ws2_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Wassilewskija
Stock Code: N1601
Growth Conditions:
locationGrowth Room
Humidity80 %
Temperature22 °C
Lighting(Source: 50 - 80 ìmol photons m-2 s-1)24 hour light
Medium0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (full-strength formulation Murashige and Skoog) . After 18 days on MS agar plants were transferred to a hydroponic system containing full strength nutrient solution containing KH2PO4 0.25mM, KOH 0.50mM, MgSO4.7H2O 0.75mM, CaCl2.2H2O 0.03mM, FeNaEDTA 0.10mM, Ca(NO3)2.4H2O 4.00mM, H3BO3 30.0µM, MnSO4.4H2O 10.0µM, ZnSO4.7H2O 1.0µM, CuSO4.5H2O 3.0µM, Na2MoO4.2H2O 0.5µM.
Stratificationimbibed for 3-5 days at 4 °C
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: Whole roots
Plant Ontology terms for this tissue type: 
Unknown PO Term!
Diseased: Normal
Other Information:
experimental_backgroundWassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: TriZOL
Method:
Protocolas per manafacturer's instructions
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol

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: 2003-11-19

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:0.319895
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:
RawQ3.55
NoiseAvg:6.02,Stdev:0.33,Max:7.1,Min:5.2
BackgroundAvg:98.45,Stdev:2.52,Max:105.9,Min:94.1
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.319895
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Hampton_1-2_akt1_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 ("Hampton_1-2_akt1_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: Hampton_1-2_akt1_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: akt1-1
Stock Code: N3762
Genetic Background: Wassilewskija
Growth Conditions:
locationGrowth Room
Humidity80 %
Temperature22 °C
Lighting(Source: 50 - 80 ìmol photons m-2 s-1)24 hour light
Medium0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (full-strength formulation Murashige and Skoog) . After 18 days on MS agar plants were transferred to a hydroponic system containing full strength nutrient solution containing KH2PO4 0.25mM, KOH 0.50mM, MgSO4.7H2O 0.75mM, CaCl2.2H2O 0.03mM, FeNaEDTA 0.10mM, Ca(NO3)2.4H2O 4.00mM, H3BO3 30.0µM, MnSO4.4H2O 10.0µM, ZnSO4.7H2O 1.0µM, CuSO4.5H2O 3.0µM, Na2MoO4.2H2O 0.5µM.
Stratificationimbibed for 3-5 days at 4 °C
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: Whole roots
Plant Ontology terms for this tissue type: 
Unknown PO Term!
Diseased: Normal
Other Information:
experimental_backgroundWassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: TriZOL
Method:
Protocolas per manafacturer's instructions
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol

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: 2003-11-19

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:0.528062
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:
RawQ3.74
NoiseAvg:5.79,Stdev:0.37,Max:7.0,Min:4.9
BackgroundAvg:110.28,Stdev:2.75,Max:120.6,Min:105.6
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.528062
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Hampton_1-3_cngc4_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 ("Hampton_1-3_cngc4_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: Hampton_1-3_cngc4_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: cngc4
Stock Code:
Growth Conditions:
locationGrowth Room
Humidity80 %
Temperature22 °C
Lighting(Source: 50 - 80 ìmol photons m-2 s-1)24 hour light
Medium0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (full-strength formulation Murashige and Skoog) . After 18 days on MS agar plants were transferred to a hydroponic system containing full strength nutrient solution containing KH2PO4 0.25mM, KOH 0.50mM, MgSO4.7H2O 0.75mM, CaCl2.2H2O 0.03mM, FeNaEDTA 0.10mM, Ca(NO3)2.4H2O 4.00mM, H3BO3 30.0µM, MnSO4.4H2O 10.0µM, ZnSO4.7H2O 1.0µM, CuSO4.5H2O 3.0µM, Na2MoO4.2H2O 0.5µM.
Stratificationimbibed for 3-5 days at 4 °C
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: Whole roots
Plant Ontology terms for this tissue type: 
Unknown PO Term!
Diseased: Normal
Other Information:
experimental_backgroundWassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: TriZOL
Method:
Protocolas per manafacturer's instructions
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol

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: 2003-11-19

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:0.543701
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:
RawQ2.70
NoiseAvg:3.91,Stdev:0.17,Max:4.4,Min:3.6
BackgroundAvg:71.40,Stdev:1.68,Max:76.5,Min:67.9
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.543701
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Hampton_1-4_cngc1_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 ("Hampton_1-4_cngc1_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: Hampton_1-4_cngc1_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: cngc1
Stock Code:
Growth Conditions:
locationGrowth Room
Humidity80 %
Temperature22 °C
Lighting(Source: 50 - 80 ìmol photons m-2 s-1)24 hour light
Medium0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (full-strength formulation Murashige and Skoog) . After 18 days on MS agar plants were transferred to a hydroponic system containing full strength nutrient solution containing KH2PO4 0.25mM, KOH 0.50mM, MgSO4.7H2O 0.75mM, CaCl2.2H2O 0.03mM, FeNaEDTA 0.10mM, Ca(NO3)2.4H2O 4.00mM, H3BO3 30.0µM, MnSO4.4H2O 10.0µM, ZnSO4.7H2O 1.0µM, CuSO4.5H2O 3.0µM, Na2MoO4.2H2O 0.5µM.
Stratificationimbibed for 3-5 days at 4 °C
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: Whole roots
Plant Ontology terms for this tissue type: 
Unknown PO Term!
Diseased: Normal
Other Information:
experimental_backgroundWassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: TriZOL
Method:
Protocolas per manafacturer's instructions
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol

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: 2003-11-19

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:0.471934
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:
RawQ4.26
NoiseAvg:6.65,Stdev:0.40,Max:7.9,Min:5.9
BackgroundAvg:125.01,Stdev:4.37,Max:137.7,Min:116.6
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.471934
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Hybridisation Set: Hampton_genome_Rep2

Slide: Hampton_1-5_ws2_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 ("Hampton_1-5_ws2_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: Hampton_1-5_ws2_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Wassilewskija
Stock Code: N1601
Growth Conditions:
locationGrowth Room
Humidity80 %
Temperature22 °C
Lighting(Source: 50 - 80 ìmol photons m-2 s-1)24 hour light
Medium0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (full-strength formulation Murashige and Skoog) . After 18 days on MS agar plants were transferred to a hydroponic system containing full strength nutrient solution containing KH2PO4 0.25mM, KOH 0.50mM, MgSO4.7H2O 0.75mM, CaCl2.2H2O 0.03mM, FeNaEDTA 0.10mM, Ca(NO3)2.4H2O 4.00mM, H3BO3 30.0µM, MnSO4.4H2O 10.0µM, ZnSO4.7H2O 1.0µM, CuSO4.5H2O 3.0µM, Na2MoO4.2H2O 0.5µM.
Stratificationimbibed for 3-5 days at 4 °C
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: Whole roots
Plant Ontology terms for this tissue type: 
Unknown PO Term!
Diseased: Normal
Other Information:
experimental_backgroundWassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: TriZOL
Method:
Protocolas per manafacturer's instructions
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol

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: 2003-11-19

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:0.45972
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:
RawQ3.11
NoiseAvg:5.06,Stdev:0.21,Max:5.7,Min:4.5
BackgroundAvg:82.17,Stdev:1.64,Max:86.5,Min:77.6
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.459720
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Hampton_1-6_akt1_Rep2_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 ("Hampton_1-6_akt1_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: Hampton_1-6_akt1_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: akt1-1
Stock Code: N3762
Genetic Background: Wassilewskija
Growth Conditions:
locationGrowth Room
Humidity80 %
Temperature22 °C
Lighting(Source: 50 - 80 ìmol photons m-2 s-1)24 hour light
Medium0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (full-strength formulation Murashige and Skoog) . After 18 days on MS agar plants were transferred to a hydroponic system containing full strength nutrient solution containing KH2PO4 0.25mM, KOH 0.50mM, MgSO4.7H2O 0.75mM, CaCl2.2H2O 0.03mM, FeNaEDTA 0.10mM, Ca(NO3)2.4H2O 4.00mM, H3BO3 30.0µM, MnSO4.4H2O 10.0µM, ZnSO4.7H2O 1.0µM, CuSO4.5H2O 3.0µM, Na2MoO4.2H2O 0.5µM.
Stratificationimbibed for 3-5 days at 4 °C
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: Whole roots
Plant Ontology terms for this tissue type: 
Unknown PO Term!
Diseased: Normal
Other Information:
experimental_backgroundWassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: TriZOL
Method:
Protocolas per manafacturer's instructions
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol

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: 2003-11-19

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:0.355346
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:
RawQ3.23
NoiseAvg:5.64,Stdev:0.27,Max:6.7,Min:5.1
BackgroundAvg:83.99,Stdev:2.98,Max:92.9,Min:76.9
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.355346
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Hampton_1-7_cngc4_Rep2_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 ("Hampton_1-7_cngc4_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: Hampton_1-7_cngc4_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: cngc4
Stock Code:
Growth Conditions:
locationGrowth Room
Humidity80 %
Temperature22 °C
Lighting(Source: 50 - 80 ìmol photons m-2 s-1)24 hour light
Medium0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (full-strength formulation Murashige and Skoog) . After 18 days on MS agar plants were transferred to a hydroponic system containing full strength nutrient solution containing KH2PO4 0.25mM, KOH 0.50mM, MgSO4.7H2O 0.75mM, CaCl2.2H2O 0.03mM, FeNaEDTA 0.10mM, Ca(NO3)2.4H2O 4.00mM, H3BO3 30.0µM, MnSO4.4H2O 10.0µM, ZnSO4.7H2O 1.0µM, CuSO4.5H2O 3.0µM, Na2MoO4.2H2O 0.5µM.
Stratificationimbibed for 3-5 days at 4 °C
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: Whole roots
Plant Ontology terms for this tissue type: 
Unknown PO Term!
Diseased: Normal
Other Information:
experimental_backgroundWassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: TriZOL
Method:
Protocolas per manafacturer's instructions
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol

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: 2003-11-19

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:0.357799
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:
RawQ3.18
NoiseAvg:5.46,Stdev:0.28,Max:6.4,Min:4.8
BackgroundAvg:87.00,Stdev:3.25,Max:94.7,Min:80.6
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.357799
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Hampton_1-8_cngc1_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Hampton_1-8_cngc1_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: Hampton_1-8_cngc1_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: cngc1
Stock Code:
Growth Conditions:
locationGrowth Room
Humidity80 %
Temperature22 °C
Lighting(Source: 50 - 80 ìmol photons m-2 s-1)24 hour light
Medium0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (full-strength formulation Murashige and Skoog) . After 18 days on MS agar plants were transferred to a hydroponic system containing full strength nutrient solution containing KH2PO4 0.25mM, KOH 0.50mM, MgSO4.7H2O 0.75mM, CaCl2.2H2O 0.03mM, FeNaEDTA 0.10mM, Ca(NO3)2.4H2O 4.00mM, H3BO3 30.0µM, MnSO4.4H2O 10.0µM, ZnSO4.7H2O 1.0µM, CuSO4.5H2O 3.0µM, Na2MoO4.2H2O 0.5µM.
Stratificationimbibed for 3-5 days at 4 °C
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: Whole roots
Plant Ontology terms for this tissue type: 
Unknown PO Term!
Diseased: Normal
Other Information:
experimental_backgroundWassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: TriZOL
Method:
Protocolas per manafacturer's instructions
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol

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: 2003-11-19

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:0.406897
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:
RawQ3.26
NoiseAvg:5.38,Stdev:0.28,Max:6.5,Min:4.6
BackgroundAvg:86.06,Stdev:2.99,Max:92.0,Min:78.4
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.406897
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Hybridisation Set: Hampton_genome_Rep3

Slide: Hampton_1-9_ws2_Rep3_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 ("Hampton_1-9_ws2_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: Hampton_1-9_ws2_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Wassilewskija
Stock Code: N1601
Growth Conditions:
locationGrowth Room
Humidity80 %
Temperature22 °C
Lighting(Source: 50 - 80 ìmol photons m-2 s-1)24 hour light
Medium0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (full-strength formulation Murashige and Skoog) . After 18 days on MS agar plants were transferred to a hydroponic system containing full strength nutrient solution containing KH2PO4 0.25mM, KOH 0.50mM, MgSO4.7H2O 0.75mM, CaCl2.2H2O 0.03mM, FeNaEDTA 0.10mM, Ca(NO3)2.4H2O 4.00mM, H3BO3 30.0µM, MnSO4.4H2O 10.0µM, ZnSO4.7H2O 1.0µM, CuSO4.5H2O 3.0µM, Na2MoO4.2H2O 0.5µM.
Stratificationimbibed for 3-5 days at 4 °C
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: Whole roots
Plant Ontology terms for this tissue type: 
Unknown PO Term!
Diseased: Normal
Other Information:
experimental_backgroundWassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: TriZOL
Method:
Protocolas per manafacturer's instructions
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol

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: 2003-11-19

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:0.444012
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:
RawQ3.11
NoiseAvg:5.12,Stdev:0.19,Max:5.6,Min:4.5
BackgroundAvg:83.95,Stdev:2.52,Max:90.9,Min:77.6
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.444012
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Hampton_1-10_akt1_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 ("Hampton_1-10_akt1_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: Hampton_1-10_akt1_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: akt1-1
Stock Code: N3762
Genetic Background: Wassilewskija
Growth Conditions:
locationGrowth Room
Humidity80 %
Temperature22 °C
Lighting(Source: 50 - 80 ìmol photons m-2 s-1)24 hour light
Medium0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (full-strength formulation Murashige and Skoog) . After 18 days on MS agar plants were transferred to a hydroponic system containing full strength nutrient solution containing KH2PO4 0.25mM, KOH 0.50mM, MgSO4.7H2O 0.75mM, CaCl2.2H2O 0.03mM, FeNaEDTA 0.10mM, Ca(NO3)2.4H2O 4.00mM, H3BO3 30.0µM, MnSO4.4H2O 10.0µM, ZnSO4.7H2O 1.0µM, CuSO4.5H2O 3.0µM, Na2MoO4.2H2O 0.5µM.
Stratificationimbibed for 3-5 days at 4 °C
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: Whole roots
Plant Ontology terms for this tissue type: 
Unknown PO Term!
Diseased: Normal
Other Information:
experimental_backgroundWassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: TriZOL
Method:
Protocolas per manafacturer's instructions
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol

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: 2003-11-19

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:0.335116
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:
RawQ3.37
NoiseAvg:6.29,Stdev:0.29,Max:7.7,Min:5.6
BackgroundAvg:87.93,Stdev:2.31,Max:95.0,Min:82.4
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.335116
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Hampton_1-11_cngc4_Rep3_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 ("Hampton_1-11_cngc4_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: Hampton_1-11_cngc4_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: cngc4
Stock Code:
Growth Conditions:
locationGrowth Room
Humidity80 %
Temperature22 °C
Lighting(Source: 50 - 80 ìmol photons m-2 s-1)24 hour light
Medium0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (full-strength formulation Murashige and Skoog) . After 18 days on MS agar plants were transferred to a hydroponic system containing full strength nutrient solution containing KH2PO4 0.25mM, KOH 0.50mM, MgSO4.7H2O 0.75mM, CaCl2.2H2O 0.03mM, FeNaEDTA 0.10mM, Ca(NO3)2.4H2O 4.00mM, H3BO3 30.0µM, MnSO4.4H2O 10.0µM, ZnSO4.7H2O 1.0µM, CuSO4.5H2O 3.0µM, Na2MoO4.2H2O 0.5µM.
Stratificationimbibed for 3-5 days at 4 °C
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: Whole roots
Plant Ontology terms for this tissue type: 
Unknown PO Term!
Diseased: Normal
Other Information:
experimental_backgroundWassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: TriZOL
Method:
Protocolas per manafacturer's instructions
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol

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: 2003-11-19

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:0.321492
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:
RawQ3.52
NoiseAvg:6.33,Stdev:0.25,Max:7.4,Min:5.7
BackgroundAvg:94.49,Stdev:1.78,Max:100.0,Min:91.0
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.321492
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015

Slide: Hampton_1-12_cngc1_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 ("Hampton_1-12_cngc1_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: Hampton_1-12_cngc1_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: cngc1
Stock Code:
Growth Conditions:
locationGrowth Room
Humidity80 %
Temperature22 °C
Lighting(Source: 50 - 80 ìmol photons m-2 s-1)24 hour light
Medium0.8 % (w/v) agar containing 1 % (w/v) sucrose and a basal salt mix (full-strength formulation Murashige and Skoog) . After 18 days on MS agar plants were transferred to a hydroponic system containing full strength nutrient solution containing KH2PO4 0.25mM, KOH 0.50mM, MgSO4.7H2O 0.75mM, CaCl2.2H2O 0.03mM, FeNaEDTA 0.10mM, Ca(NO3)2.4H2O 4.00mM, H3BO3 30.0µM, MnSO4.4H2O 10.0µM, ZnSO4.7H2O 1.0µM, CuSO4.5H2O 3.0µM, Na2MoO4.2H2O 0.5µM.
Stratificationimbibed for 3-5 days at 4 °C
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)3.90
Tissue: Whole roots
Plant Ontology terms for this tissue type: 
Unknown PO Term!
Diseased: Normal
Other Information:
experimental_backgroundWassilewskija -2 (N1601)akt1-1 (N3762)Hirsch RE, Lewis BD, Spalding EP, Sussman MR. 1998. A role for the AKT1 potassium channel in plant nutrition. Science 280:918-921.cngc1 and cngc4 were obtained from the Wisconsin T-DNA knockout facility: Sussman MR, Amasino RM, Young JC, Krysan PJ, Austin-Phillips S. 2000. The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiology 124:1465-1467.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: TriZOL
Method:
Protocolas per manafacturer's instructions
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol

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: 2003-11-19

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:0.28419
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:
RawQ5.34
NoiseAvg:12.89,Stdev:0.47,Max:14.7,Min:11.3
BackgroundAvg:143.09,Stdev:2.89,Max:152.7,Min:136.6
Gamma1H0.0025
Gamma2L0.003
Gamma2H0.003
TGT100
Perturbation1.1
SF0.284190
Alpha10.04
Alpha20.06
SFGeneAll
NF1.000000
BF
Gamma1L0.0025
Tau0.015


Problems? Comments? Suggestions? Contact the Affymetrix Team