Next Generation Sequencing Facilitates Quantitative Analysis of the Role of nuclear protein DEK in hematopoietic stem cells [RNA-seq]

Purpose:To identify genes and the molecular pathways involved in the DEK regulating hematopoietic stem cells (HSC) in mice, we performed RNA-Sequence of HSC freshly sorted from mice. Methods: mRNA profiles of HSC in Dekfl/fl (floxp) and Dekfl/fl,Tie2-Cre (cKO) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. Results:Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the mouse genome (build mm10) and identified 33299 transcripts in HSC (the floxp and cKO group) with BWA workflow. Conclusions: Our results represent the first detailed analysis of HSC transcriptomes in Dek-knockout mice and found that DEK regulated multiple mRNA pathways in HSC. The mRNA profiles of HSC in Control and Dek-knockout mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.