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Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags

Authors :
Haizhou Tang
James K. Bonfield
Jane Rogers
Christopher Hyland
Ian M. Overton
Matthew D. Francis
Ewan Birney
Simon J. Hubbard
William Brown
Joan Burnside
Darren Grafham
Sam Griffiths-Jones
Michael D. R. Croning
Kevin J. Beattie
Carol Scott
Robert L. Davies
Sean Humphray
Elizabeth R. Farrell
Ruth Taylor
Stuart A. Wilson
Paul E. Boardman
Stuart McLaren
Cheryll Tickle
Source :
Hubbard, S J, Grafham, D V, Beattie, K J, Overton, I M, McLaren, S R, Croning, M D R, Boardman, P E, Bonfield, J K, Burnside, J, Davies, R M, Farrell, E R, Francis, M D, Griffiths-Jones, S, Humphray, S J, Hyland, C, Scott, C E, Tang, H, Taylor, R G, Tickle, C, Brown, W R A, Birney, E, Rogers, J & Wilson, S A 2005, ' Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags ', Genome Research, vol. 15, no. 1, pp. 174-183 . https://doi.org/10.1101/gr.3011405
Publication Year :
2004

Abstract

We present an analysis of the chicken (Gallus gallus) transcriptome based on the full insert sequences for 19,626 cDNAs, combined with 485,337 EST sequences. The cDNA data set has been functionally annotated and describes a minimum of 11,929 chicken coding genes, including the sequence for 2260 full-length cDNAs together with a collection of noncoding (nc) cDNAs that have been stringently filtered to remove untranslated regions of coding mRNAs. The combined collection of cDNAs and ESTs describe 62,546 clustered transcripts and provide transcriptional evidence for a total of 18,989 chicken genes, including 88% of the annotated Ensembl gene set. Analysis of the ncRNAs reveals a set that is highly conserved in chickens and mammals, including sequences for 14 pri-miRNAs encoding 23 different miRNAs. The data sets described here provide a transcriptome toolkit linked to physical clones for bioinformaticians and experimental biologists who wish to use chicken systems as a low-cost, accessible alternative to mammals for the analysis of vertebrate development, immunology, and cell biology.

Details

ISSN :
10889051
Volume :
15
Issue :
1
Database :
OpenAIRE
Journal :
Genome research
Accession number :
edsair.doi.dedup.....fa47989cb1f14ceb68530e8dc89f41c7
Full Text :
https://doi.org/10.1101/gr.3011405