The study profiled the effect of Phf6 deletion on gene expression in hematopoietic stem cells (HSCs), multipotent progenitor cells (MPPs) and hematopoietic progenitor cells (HPC-1). Phf6lox/Y;Tie2-creTg/+ mice were prepared on a C57BL/6 background so that Phf6 deletion could be selectively mediated by Tie2-cre. Cell populations were sorted from bone marrow samples using standard surface markers  (LinSCA1+cKIT+(LSK) CD150+ CD48 for HSCs, LinSCA1+cKIT+(LSK) CD150 CD48 for MPPs and LinSCA1+cKIT+(LSK) CD150- CD48+ for HPC-1 cells). Phf6 intact and Phf6-delected cells of all three types were profiled by paired-end RNA-seq using an Illumina NextSeq 500 sequencer. RNA-seq libraries were prepared from the HPC-1 samples used a standard Illumina TruSeq library protocol whereas the libraries for the HSC and MPP samples used a SMART-seq ultra low input kit for cDNA synthesis and amplification. Statistical analysis of the TruSeq and SMART-seq samples was undertaken separately. SOURCE: Alexandra Garnham (garnham.a@wehi.edu.au) -  Walter and Eliza Hall Institute of Medical Research

Pluto Bioinformatics

GSE126316: RNA-seq profiling of HSC, MPPs and HPC-1s from Phf6-deleted and Phf6-intact mice