Transcriptome landscape of human primary monocytes at different sequencing depth
Document Type
Article
Publication Date
1-1-2017
Abstract
Differential gene and transcript expression pattern of human primary monocytes from healthy young subjects were profiled under different sequencing depths (50M, 100M, and 200M reads). The raw data consisted of 1.3 billion reads generated from RNA sequencing (RNA-Seq) experiments. A total of 17,657 genes and 75,392 transcripts were obtained at sequencing depth of 200M. Total splice junction reads showed an even more significant increase. Comparative analysis of the expression patterns of immune-related genes revealed a total of 217 differentially expressed (DE) protein-coding genes and 50 DE novel transcripts, in which 40 DE protein-coding genes were related to the immune system. At higher sequencing depth, more genes, known and novel transcripts were identified and larger proportion of reads were allowed to map across splice junctions. The results also showed that increase in sequencing depth has no effect on the sequence alignment.
Keywords
RNA sequencing, Transcriptome, Monocytes, Sequencing depth
Divisions
InstituteofBiologicalSciences
Funders
Ministry of Higher Education Malaysia - University of Malaya High Impact Research (HIR) Grant: UM.S/P/HIR/MOHE/30,Ministry of Higher Education Malaysia Fundamental Research Grant Scheme (FRGS): FP050-2016,University of Malaya Research Grant (UMRG): RP004C-13AFR
Publication Title
Genomics
Volume
109
Issue
5-6
Publisher
Elsevier