Description

• Title:
  Data set for transcriptome analysis of liver in cattle breeds
• Creator:
  Sachajko, Mateusz;
  Herudzińska, Magdalena;
  Jaskowski, Jedrzej M.;
  Szczepanek, Joanna;
  Buszewska-Forajta, Magdalena;
  Feng, Yaping;
  Kumar, Dibyendu;
  Pareek, Chandra Shekhar
• Description:
  Transcriptome analysis using high-throughput next-generation sequencing (HT-NGS) technology provides the capability to understand global gene expression variations through a wide range of tissue samples in domesticated animals. We provide raw and analysed data for transcriptomic analysis of liver tissues from Polish-HF, Polish Red and Hereford cattle breeds, obtained by RNA-seq. High-quality sequencing data have been analysed using our bioinformatics pipeline which consists of FastQC for quality controls, Trimmomatic for trimming, and BWA version 0.7.5-r404 for alignment to the Bos taurus reference genome, SAMtools for SNPs identifications, and differentially expressed genes (DEGs) identification using DEseq and edgeR pipelines after adjustment for false-discovery rate (FDR) with adjusted two-sided p values <0.01 and the trimmed mean of M values (TMM) normalisation method. The data accompanying the published manuscript describing the SNPs and DEGs identification in the bovine liver transcriptome of cattle breeds. Raw FASTq files for the RNA-seq libraries are deposited in the NCBI Sequence Read Archive (SRA) and have been assigned BioProject accession PRJNA312148. Raw and processed RNA-seq data were deposited and made publicly available on the Gene Expression Omnibus (GEO; GSE114233).
• Object availability:
  free access
• Rights:
  Prawa autorskie (c) 2020 Translational Research In Veterinary Science
• Date:
  2020.01.16
• Type:
  info:eu-repo/semantics/article;
  info:eu-repo/semantics/publishedVersion
• Language:
  English
• Source:
  Translational Research in Veterinary Science; Vol. 2 No. 2 (2019); 51-56;
  Translational Research In Veterinary Science; Tom 2 Nr 2 (2019); 51-56;
  2657-4489
• Format:
  application/pdf
• Publisher:
  Nicolaus Copernicus University in Toruń
• Relation: https://apcz.umk.pl/TRVS/article/view/TRVS.2019.009/24477
• Subject:
  RNA-seq;
  cattle;
  liver;
  breeds;
  NGS;
  SNPs;
  DEGs;
  DEseq;
  EdgeR;
  FDR;
  SAMtools;
  BWA;
  FASTq;
  SRA;
  NCBI;
  GEO
• Identifier: https://apcz.umk.pl/TRVS/article/view/TRVS.2019.009
• Data provider:
  Akademicka Platforma Czasopism
• Can I use it?:
  seek permission
• Type:
  text