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A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning
james hadfield, Genome (james.hadfield@bbsrc.ac.uk)
Experiment design (4 hybridizations)
genotype
•rar1-2 (mutant) •Sultan 5 (wild type)

Trancript Based Cloning (TBC) uses standard Gene Expression techniques to quickly isolate genes of interest and begin to determine their function. ...[complete overview]

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Experiment Name: A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning
Accession No: BB5
Microarray: Barley1
Visibility: public
Experiment Type:
Experiment Factor(s):
genotype
•rar1-2 (mutant)  •Sultan 5 (wild type)
Quality Control: biological replicates
Treatment summary:
 genotype  # replicates
 rar1-2 (mutant)  2
 Sultan 5 (wild type)  2
Total hybridizations: 4
Description: Trancript Based Cloning (TBC) uses standard Gene Expression techniques to quickly isolate genes of interest and begin to determine their function. Using a particular mutant phenotype, identified during a programme of mutagenesis and screning, and a wild-type control we can quickly determine a list of genes that is likely to contain the gene responsible for the phenotype.
TBC is a general method for identifying and cloning important plant genes that is fast and may be applicable to almost any plant species
Transcript abundance assays on the barley rar1-2 mutant and Sultan5 wild type were performed by using standard methods for the Affymetrix barley genome array (Affymetrix). For each genotype, two independent biological replicates were analyzed and pooled for analysis.
Data were analyzed with DCHIP VERSION 1.3 (www.dchip.org),using data from only perfect-match oligonucleotides. Model-based analysis was performed by using perfect match-only analysis, compiling data from two biological replicates for each condition. Pairwise comparisons were analyzed for each condition, and a lower 90% confidence bound (LCB) and fold change were determined for each comparison. Gene expression changes were considered significant if the LCB was 1.4-fold or higher and if the intensities between the two conditions differed by >100.

Submitted at NCBI GEO via PLEXdb.

Publication: 'A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning', Mitra RM, Gleason CA, Edwards A, Hadfield J, Downie JA, Oldroyd GE, Long SR
Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4701-5
pubmed: 15070781
Created: 2004-07-29 10:12:19
Last Update: 2008-08-05 11:40:05
GEO Accession GSE33397
Submitter: james e hadfield
Name: james hadfield
Institution: Genome
Head of Laboratory:
email(s):
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