Next Generation Sequencing Facilitates Quantitative Analysis of Human Pluripotent Stem Cell-Derived Hematopoietic Cell Transcriptomes

Next-generation sequencing (NGS) has significantly advanced the elucidation of developmental signaling mechanisms that are important for different cell lineage formation from human pluripotent stem cells (hPSCs). We report here the application of RNA-sequencing technology for transcriptome profile of hPSC-derived hematopoietic cells, and compare to those of other cell lineages including hPSCs, mesoderm, primary aorta-gonad-mesonephros (AGM) cells and cord blood hematopoietic stem cells (HSCs). IIIumina HiSeq 2X150 bp sequencing was performed on three hematopoietic cell samples from three hPSC lines by GENEWIZ. The resulting sequence reads (about 34 million reads per sample) were mapped to human genome (hg19) using HISAT, and the RefSeq transcript levels (RPKMs) were quantified using the python script rpkmforgenes.py. Our RNA-seq data confirmed the stable expression of key hematopoietic cell markers including CD45, RUNX1, CD34 and HOXA clusters, and the gene set enrichment analysis (GSEA) showed enrichment in “aorta development”, “cell migration”, “hematopoietic stem cell proliferation”, “Notch signaling regulation”, et al. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to hematopoietic function. This study presented a detailed analysis of hematopoietic transcriptomes generated by RNA-seq technology, providing insight into the mechanisms underlying the differentiation of hPSCs into hematopoietic cells. Hematopoietic transcriptome profiles of 3 different samples from 3 hPSC lines were generated by RNA-seq technology using IIIumina HiSeq