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A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning

Experiment Name: A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning
Accession No. & GeneChip: BB5, Barley1
Submitter: james e hadfield
Experiment Type: transcript based cloning
Experiment Factor: genotype
Number of Replicates: 2
Quality Control Steps: biological replicates
Quality Control Description: None
Publication_id: PubMed: 15070781
Mitra et al: "A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning" Proc Natl Acad Sci USA. 101(13):4701-5, 30 March 2004.
Last Update Time: 2004-07-29 10:12:19
Expression Data
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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.
Providers:
Name: james hadfield
Institution: Genome
Head of Laborotary:
email:
james.hadfield@bbsrc.ac.uk
Homepage:

 
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