Data set for transcriptome analysis of pituitary galnd in cattle breeds
DOI:
https://doi.org/10.12775/TRVS.2019.010Keywords
RNA-seq, cattle, pituitary gland, breeds, NGS, SNPs, SAMtools, BWA, FastQC, SRA, NCBIAbstract
Transcriptome data presented in this article is associated with the research article entitled “Single nucleotide polymorphism discovery in bovine pituitary gland using RNA-seq technology” published in PLOS One [1]. Herein, we provide raw and analysed RNA-seq data of pituitary gland tissues from three cattle breeds, viz., Polish-HF, Polish Red and Hereford cattle breeds. Bioinformatics pipelines of high-quality RNA-seq data includes the FastQC tools for quality controls, Trimmomatic cutadapt tools for trimming RNA-seq data, and BWA version 0.7.5-r404 for mapping and alignment to the Bos taurus reference genome, SAMtools for SNPs identifications in bovine pituitary gland transcriptome. Raw FASTq files for the RNA-seq libraries of bovine pituitary gland were deposited in the NCBI Sequence Read Archive (SRA) and have been assigned BioProject accession PRJNA312148.
References
Pareek CS, Smoczyński R, Kadarmideen HN, Dziuba P, Błaszczyk P, Sikora M, Walendzik P, Grzybowski T, Pierzchała M, Horbańczuk J, Szostak A, Ogluszka M, Zwierzchowski L, Czarnik U, Fraser L, Sobiech P, Wąsowicz K, Gelfand B, Feng Y, Kumar D. Single Nucleotide Polymorphism Discovery in Bovine Pituitary Gland Using RNA-Seq Technology. PLoS One. 2016;11:e0161370.
Zhao Y, Wang K, Wang WL, Yin TT, Dong WQ, Xu CJ. A high-throughput SNP discovery strategy for RNA-seq data. BMC Genomics. 2019;20:160.
Djari A, Esquerré D, Weiss B, Martins F, Meersseman C, Boussaha M, Klopp C, Rocha D. Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing. BMC Genomics. 2013;14:307.
Stothard P, Choi JW, Basu U, Sumner-Thomson JM, Meng Y, Liao X, Moore SS. Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics. 2011;12:559.
Cánovas A, Rincon G, Islas-Trejo A, Wickramasinghe S, Medrano JF. SNP discovery in the bovine milk transcriptome using RNA-Seq technology. Mamm Genome. 2010;21:592-8.
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60.
Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics, 2015;1:166-169.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. 1000 Genome Project Data Processing Subgroup. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics. 2009;25:2078-2079.
Downloads
Published
How to Cite
Issue
Section
License
Title, logo and layout of TR in VS are reserved trademarks of TR in VR.
Stats
Number of views and downloads: 554
Number of citations: 0
