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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|
|Number of Replicates:||2|
|Quality Control Steps:||biological replicates|
|Quality Control Description:||None|
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|
Access & Analysis:
Please select one action:
1. Batch download all data files at Download Center .
2. Browse Hybridizations and boxplots from experiment.
3. Visualization of hybridizations or treatment means with scatterplots and MvA plots.
4. Browse Samples from experiment.
5. Create Gene List by filter probe sets for differentially-expressed genes.
6. Pattern Recognition on filtered gene list.
|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.
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