A Large Database of Chicken Bursal ESTs as a Resource for the Analysis of Vertebrate Gene Function

Abdrakhmanov, Igor; Lodygin, Dmitry; Geroth, Paul; Arima, Hiroshi; Law, Andy; Plachý, Jiřı́; Korn, Berndt; Buerstedde, Jean-Marie

doi:10.1101/gr.1137900

Cited by 13 publications

(3 citation statements)

References 22 publications

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“…To identify candidate proteins, peptides were matched via MASCOT and/or MS-Tag to products from the chicken genome as well as the mouse, rat and/or human genomes since the chicken database is incomplete. To increase the stringency of the identification process, candidates were further compared against the bursal expressed sequence tag database 17 to ensure that the corresponding genes are transcribed in bursal B cells. Proteins identified by database searching that meet these criteria are displayed in Table 2.…”

Section: Resultsmentioning

confidence: 99%

New Approach for Analysis of the Phosphotyrosine Proteome and Its Application to the Chicken B Cell Line, DT40

et al. 2004

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In this study, we have begun to analyze phosphotyrosyl and associated proteins present in a DT40 chicken B cell line overexpressing the nonreceptor protein-tyrosine kinase, Syk. An anti-phosphotyrosine antibody was used to select tyrosine-phosphorylated proteins. After tryptic digestion, peptides were subjected to a beta-elimination reaction and phosphotyrosine-containing peptides were enriched via immobilized metal affinity chromatography. Several known substrates and candidate substrates for Syk and the location of 22 tyrosine phosphorylation sites were identified.

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Section: Resultsmentioning

confidence: 99%

New Approach for Analysis of the Phosphotyrosine Proteome and Its Application to the Chicken B Cell Line, DT40

et al. 2004

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“…To allow the electronic retrieval of chicken cDNA sequences of interest, a large database of ESTs from bursal lymphocytes is imbedded into the DT40 web site (http:// genetics.hpi.uni-hamburg.de/dt40Est.html). The first version of the database included about 7000 sequences derived from a bursal cDNA library named dkfz426 (8). In the meantime another 3000 sequences from this library have been added to the database.…”

Section: The Bursal Est Databasementioning

confidence: 99%

The DT40 web site: sampling and connecting the genes of a B cell line

Buerstedde

Arima²,

Watahiki³

et al. 2002

Nucleic Acids Research

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Thousands of new vertebrate genes have been discovered and genetic systems are needed to address their functions at the cellular level. The chicken B cell line DT40 allows efficient gene disruptions due to its high homologous recombination activity. However, cloning the gene of interest is often cumbersome, since relatively few chicken cDNA sequences are present in the public databases. In addition, the accumulation of multiple mutations within the same cell clone is limited by the consumption of one drug-resistance marker for each transfection. Here, we present the DT40 web site (http://genetics.hpi.uni-hamburg.de/dt40.html), which includes a comprehensive database of chicken bursal ESTs to identify disruption candidate genes and recyclable marker cassettes based on the loxP system. These freely available resources greatly facilitate the analysis of genes and genetic networks.

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“…Due to the complexity of the chicken genome, a high percentage of the sequences is still missing. There are studies of expressed sequence tags (EST) in chickens (Spike et al, 1996;Abdrakhmanov et al, 2000;Tirunagaru et al, 2000;Carre et al, 2006). These chicken EST clones have contributed greatly to the understanding of the chicken genome.…”

Section: Introductionmentioning

confidence: 99%

The Expression of Genes Related to Egg Production in the Liver of Taiwan Country Chickens

Ding¹,

Ko²,

Ou³

et al. 2008

Asian Australas. J. Anim. Sci

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The purpose of this study was to detect expression of genes related to egg production in Taiwan Country chickens by suppression subtractive hybridization. Liver samples of mRNA extraction from two Taiwan Country chicken strains (L2 and B), originated from the same population but with very distinct egg production rates after long-term selection for egg and meat production respectively. Two-way subtraction was performed. The hepatic cDNA from the low egg production chickens (B) was subtracted from the hepatic cDNA from the high egg production strain (L2). The reversed subtraction (L2 from B) was also performed. The resulting differentially expressed gene fragments were cloned and sequenced. We sequenced 288 clones from the forward subtraction and 96 clones from the reverse subtraction. These genes were subjected to further screening to confirm the differential expression between the two genetic breeds of chickens. The apolipoprotein B (apoB) was expressed to a greater extent in the liver of the L2 than in the B line chickens. The 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (PURH) was expressed to a greater extent in the liver of the B than in the L2 strain chickens. We demonstrated that both apoB and PURH were more highly expressed in the liver than that in other tissues (muscle, ovary, and oviduct) in laying Taiwan Country chickens. Taken together, these data suggest that after the selection for egg production, expression of apoB and PURH genes were also changed. Whether the changed expression of these genes is directly related to egg production is not known, but these two genes may be useful markers for egg laying performance in Taiwan Country chickens.

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A Large Database of Chicken Bursal ESTs as a Resource for the Analysis of Vertebrate Gene Function

Cited by 13 publications

References 22 publications

New Approach for Analysis of the Phosphotyrosine Proteome and Its Application to the Chicken B Cell Line, DT40

New Approach for Analysis of the Phosphotyrosine Proteome and Its Application to the Chicken B Cell Line, DT40

The DT40 web site: sampling and connecting the genes of a B cell line

The Expression of Genes Related to Egg Production in the Liver of Taiwan Country Chickens

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