Chicken genomics resource Edit

Citations: 35

z-index: 2.92

Basic information
Short name Chicken genomics resource
Full name Chicken genomics resource
Description Its accessibility, unique evolutionary position, and recently assembled genome sequence have advanced the chicken to the forefront of comparative genomics and developmental biology research as a model organism.
URL http://cogburn.dbi.udel.edu
Year founded 2006
Last update & version
Availability Free to academic users only
Contact information
University/Institution hosted University of Delaware
Address Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA
City Newark
Province/State Delaware
Country/Region United States
Contact name Larry A Cogburn
Contact email cogburn@udel.edu
Data information
Data object
  • Animal
Data type
  • DNA
Database category
  • Gene genome and annotation
  • Expression
Major organism
  • Gallus gallus
Keyword
  • EST sequence
Publications
  • Chicken genomics resource: sequencing and annotation of 35,407 ESTs from single and multiple tissue cDNA libraries and CAP3 assembly of a chicken gene index. [PMID: 16554550]
    Wilfrid Carre, Xiaofei Wang, Tom E Porter, Yves Nys, Jianshan Tang, Erin Bernberg, Robin Morgan, Joan Burnside, Samuel E Aggrey, Jean Simon, Larry A Cogburn,

    Its accessibility, unique evolutionary position, and recently assembled genome sequence have advanced the chicken to the forefront of comparative genomics and developmental biology research as a model organism. Several chicken expressed sequence tag (EST) projects have placed the chicken in 10th place for accrued ESTs among all organisms in GenBank. We have completed the single-pass 5'-end sequencing of 37,557 chicken cDNA clones from several single and multiple tissue cDNA libraries and have entered 35,407 EST sequences into GenBank. Our chicken EST sequences and those found in public databases (on July 1, 2004) provided a total of 517,727 public chicken ESTs and mRNAs. These sequences were used in the CAP3 assembly of a chicken gene index composed of 40,850 contigs and 79,192 unassembled singlets. The CAP3 contigs show a 96.7% match to the chicken genome sequence. The University of Delaware (UD) EST collection (43,928 clones) was assembled into 19,237 nonredundant sequences (13,495 contigs and 5,742 unassembled singlets). The UD collection contains 6,223 unique sequences that are not found in other public EST collections but show a 76% match to the chicken genome sequence. Our chicken contig and singlet sequences were annotated according to the highest BlastX and/or BlastN hits. The UD CAP3 contig assemblies and singlets are searchable by nucleotide sequence or key word (http://cogburn.dbi.udel.edu), and the cDNA clones are readily available for distribution from the chick EST website and clone repository (http://www.chickest.udel.edu). The present paper describes the construction and normalization of single and multiple tissue chicken cDNA libraries, high-throughput EST sequencing from these libraries, the CAP3 assembly of a chicken gene index from all public ESTs, and the identification of several nonredundant chicken gene sets for production of custom DNA microarrays.

    Physiol. Genomics 2006:25(3)

    35 Citations (from Europe PMC, 2018-12-08)

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  • Created on: 2018-02-13
    • ***d@***c.cn [2018-03-08]

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