Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags.
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.
Hubbard
Simon J
SJ
Faculty of Life Sciences, The University of Manchester, Manchester, M60 1QD, United Kingdom.
Grafham
Darren V
DV
Beattie
Kevin J
KJ
Overton
Ian M
IM
McLaren
Stuart R
SR
Croning
Michael D R
MD
Boardman
Paul E
PE
Bonfield
James K
JK
Burnside
Joan
J
Davies
Robert M
RM
Farrell
Elizabeth R
ER
Francis
Matthew D
MD
Griffiths-Jones
Sam
S
Humphray
Sean J
SJ
Hyland
Christopher
C
Scott
Carol E
CE
Tang
Haizhou
H
Taylor
Ruth G
RG
Tickle
Cheryll
C
Brown
William R A
WR
Birney
Ewan
E
Rogers
Jane
J
Wilson
Stuart A
SA
D000818:Animals; D002645:Chickens / Q000235:genetics*; D003001:Cloning, Molecular / Q000379:methods; D019295:Computational Biology / Q000379:methods; D018076:DNA, Complementary / Q000235:genetics* / Q000502:physiology; D020224:Expressed Sequence Tags; D015723:Gene Library; D006801:Humans; D035683:MicroRNAs / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D014158:Transcription, Genetic / Q000235:genetics*
D018076:DNA, Complementary; D035683:MicroRNAs; D022661:RNA, Untranslated