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2012 (Vol. 4, Issue: 4)
Article Information:

Ubiquitous Expression of Genes in tissues of Goat (Capra hircus) Using RNA-seq

Upasna Sharma, Priyanka Banerjee, Jyoti Joshi and Ramesh Kumar vijh
Corresponding Author:  Ramesh Kumar Vijh 

Key words:  Capra hircus , differential gene expression, gene ontology, RNA-Seq, transcriptome, ,
Vol. 4 , (4): 292-302
Submitted Accepted Published
June 19, 2012 July 09, 2012 August 20, 2012
Abstract:

Since very little information is available on goat transcriptome (only few sequenced genes and ESTs are available in the database), our main aim was to analyze the goat transcriptome for identification of ubiquitous genes through RNA-Seq approach, expression of genes across tissues and analyse the functional pathways which these highly expressed genes follow. RNA-Seq analysis was carried out on 10 tissues of Osmanabadi goats. The data was 2x76 base pair paired end reads generated using Illumina Genome Analyser GAIIx. More than 40 million reads per tissue were generated. The data was mapped using CLC Genomics Workbench on Ensembl cattle (Btau_4.0) genes version 62 downloaded from BioMart. The mapping statistics was discerned for each of the mapped gene for all the 10 tissues. There was a great deal of homology between the genes of cattle and goats and this was expected as both are ruminants and phylogenetically close to one another. The expression profile for genes of each of the 10 tissues was calculated in terms of RPKM values. The differential expression of genes among the different tissues was carried out using 3 algorithms. The genes common among the 3 algorithms were associated with GO IDs and the functional annotation was carried out by estimating the GO term occurrences using CateGOrizer web server. The study revealed that more than 75% genes are ubiquitously expressed (expressed in all tissues) with very limited number of tissue specific genes based on expression values (expressed in only one tissue). These genes are mostly related with the specific functions performed by various tissues.
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  Cite this Reference:
Upasna Sharma, Priyanka Banerjee, Jyoti Joshi and Ramesh Kumar vijh, 2012. Ubiquitous Expression of Genes in tissues of Goat (Capra hircus) Using RNA-seq.  International Journal of Animal and Veterinary Advances, 4(4): 292-302.
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ISSN (Online):  2041-2908
ISSN (Print):   2041-2894
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