Bovine RNA-seq Data Analysis of Liver and Pituitary Gland
Poster May 12, 2015
Pareek CS12, Smoczynski R12, Dziuba P12, Sikora M12, Golebiewski M2, Blaszczyk P12, Gelfand B3, Yaping F3, Kumar D3.
An experimental design representing young growing bulls of three cattle breeds at three different developmental ages were sequenced in context to bovine body growth and developmental trait using Illumina NextSeq platform. Approximately 40-50 million paired-end reads were obtained per library (n=36). For each tissue, 18 breed-specific and age dependent-specific libraries were sequenced. Using a computational pipeline, tissue-specific transcripts were mapped to bovine reference genome (UMD3.1 assembly). Mapping tools (https://github.com/alexdobin/STAR/releases) was used to align the reads to the reference cattle genome. Results of transcriptome mapping of liver in Polish Red bulls revealed 98.88% mapping reads (400453035 map reads out of 408045666) and transcriptome mapping of pituitary gland in Hereford bulls revealed 97.80% mapping reads (337471226 map reads out of 345069302). However, paired end transcripts of pituitary gland (Hereford) and liver (Polish red) were properly paired @ of 82.22% and 79.56% respectively. Study provides a glimpse into the tissue specific mRNA content of bovine pituitary gland and liver which will eventually facilitate future experimental trait-associated studies to unravel the putative ESTs and/or causal SNPs for bovine body growth and developmental process.
Despite the developments in conventional PCR, the complexity of multiplex Real Time PCR is still limited due to the lack of sufficient detection channels. To achieve high-end multiplexing capacity on standard Real Time PCR machines, Anapa Biotech has developed the MeltPlex® technology (see box on right).READ MORE