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Comments on Kohara Y et al. (1995) International C. elegans Meeting "THE C.ELEGANS cDNA PROJECT: TOWARDS AN EXPRESSION MAP OF THE GENOME" (0)
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Kohara Y, Motohashi T, Tabara H, Sugimoto A, & Watanabe H (1995). THE C.ELEGANS cDNA PROJECT: TOWARDS AN EXPRESSION MAP OF THE GENOME presented in International C. elegans Meeting. Unpublished information; cite only with author permission.
Aiming to ultimately understand the network of gene expression in development of the worm, we are constructing an expression map of the 100Mb genome through identifying and characterizing all of its cDNA species, whose number is estimated to be around 15,000. 36,000 cDNA clones were picked up randomly from 3 different cDNA libraries (from size-fractionated (>2Kb) and unfractionated cDNA from a mixed-stage population, and from embryos) and have been subjected to (1) tag-sequencing from both 5'- and 3'- ends, (2) mapping onto the genome, and (3) analysis of expression pattern. After the analysis of every some 4,000 clones, cDNA species which were represented by more than 4 clones in the previous analysis were removed to minimize the redundancy of analyses. (1) Tag sequencing The 3'-tag sequences were compared each other by FASTA to classify the cDNA clones into unique groups (genes). Thus far, 8,305 clean 3'-tag sequences were obtained, which were classified into 3,496 unique cDNA groups (assigned CELK00001 through CELK03500). This analysis also detected many pairs of clones which appeared to be generated by alternative splicing or differential poly-A addition. In BLASTX search of the 5'- tags, 36% of the cDNA groups showed significant similarities (blastx score > 100). (2) Mapping onto the genome Using the YAC polytene filters, 1,416 cDNA groups have been mapped onto the genome. Mapping in silico using the cosmid sequences available at the Sanger Centre was also effective. (3) Analysis of expression pattern We have developed a method of in situ hybridization on whole mount embryos of the multi-well format (see the poster by H. Tabara et al.), and we are applying the method to the set of representative clones of the identified cDNA groups.
