BBSRC ChickEST Database

Disclaimer: this web-site is no longer actively maintained, so some of the information contained may be out of date. We hope its still of use and we intend to keep it up and running, but can not guarantee this indefinitely

This legacy web-site provides access to 339,314 Gallus gallus ESTs which were sequenced from 64 cDNA libraries generated from 21 different embryonic and adult tissues (sequence stats + tissue list). These ESTs have been clustered into 64,760 gene-bins which were assembled into 85,486 contiguous sequences (contigs). For each tissue, we constructed one standard and at least two normalised libraries. The only exception to this is the adult adipose tissue, for which normalisation failed completely.

New Additions
Sept. 2004 Based on UniProt dataset, 9,137 cDNAs have been assigned a GO term by passing through our annotation pipeline. The data can de downloaded here.
Aug. 2004 A set of putative 786 chicken antisense transcripts are predicted, based on Exonerate matches of the cDNAs to the chicken genome sequence. These clones are found to be exclusively antisense to an Ensembl chicken gene. Get the data from here.
July 2004 19,626 annotated finished cDNA sequences including a set of 2260 full length cDNAs are available from our FTP site and are searchable using NCBI BLAST on this site
March 16th 2004 High-confidence SNP data now available from the FTP site. This corresponds to the set generated last summer, that have now been submitted to dbSNP and mapped against the current genome assembly added to site.
Jan 5th 2004 RNAi target sequence prediction tool added to site.
July 10th 2003 An in-silico subtraction system is being developed here for use with the chicken EST data. This will provide a method for selecting interesting clones for experiments such as in-situ hybridisations (see the FAQ entry for more details).
July 3rd 2003 A set of 11,000 high-confidence single nucleotide polymorphisms (SNPs) have been predicted using various filtering criteria and the Polybayes program. These are searchable via the SNPs section of this web-site and are highlighted as red-triangles on the contig overview images (e.g. 335413.6)

Our FTP site, ftp://www.chick.manchester.ac.uk, contains the following data for download :-

Please cite 'Boardman PE, Sanz-Ezquerro J, Overton IM, Burt DW, Bosch E, Fong WT, Tickle C, Brown WRA, Wilson SA and Hubbard SJ. A Comprehensive Collection of Chicken cDNAs. Current Biology 2002 12:1965-1969.' when using the EST data. [Medline] and Hubbard SJ, Grafham DV, Beattie KJ, Overton IM, McLaren SR, Croning MDR, Boardman PE, Bonfield JK, Burnside J, Davies RM, Farrell ER, Francis MD, Griffiths-Jones S, Humphray SJ, Hyland C, Scott CE, Tang H, Taylor RG, Tickle C, Brown WRA, Birney E, Rogers J, and Wilson SA Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags Genome Res. 2005 15: 174-183, [Medline]for cDNA and other info.

We believe clones are available to order via here

For further information please email Dr Simon Hubbard