RNA-Seq Data Analysis of Bovine Liver and Pituitary Transcriptome

High-throughput transcriptome analysis of bovine liver and pituitary gland was performed to characterize the in-depth understanding of transcriptome assembling.With its ability to provide deep coverage and base-pair resolution RNA sequencing is a very powerful technique to study gene expression and their dynamics in an unbiased way. Here we present transcriptome data from Hereford Bulls to measure gene expression in liver and pituitary gland tissues. Fifteen tissue samples each from liver and pituitary gland tissues of young Hereford bulls were analyzed using the Illumina MiSeq system. Out of over 30 million reads, 29,979,879 reads are of high quality. The reads were aligned with Bowtie using default settings against both Bull and Cow genome assembly. Roughly, 50% of mapped reads belongs to unanchored chromosome. Fast quality control (FastQC) and PRINSEQ analysis revealed the sequence read lengths ranged from 35-251 bp size with more than 50% of all reads with length over 200bp and 10% of reads below 100bp. FastQC results further revealed 1) good FastQC scoring results for basic statistic, per sequence quality score and per base N content, 2) warning FastQC scoring results for sequencing length distribution, over presented sequences; 3) bad FastQC scoring results for per base sequence quality, per base sequence content, per base GC content, sequence duplication levels and Kmer content, respectively. The FastQC results revealed rapid per base read quality decrease with longer sequences. Even with preprocessing step of read quality trimming and sequence filtration, the mapping result showed the low coverage (~ 25%) of Hereford liver and pituitary transcriptome.