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

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

PROVIDER: PRJNA521533 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8551170_1.fastq.gz	Fastqsanger.gz
	SRR8551170_2.fastq.gz	Fastqsanger.gz
	SRR8551180_1.fastq.gz	Fastqsanger.gz
	SRR8551180_2.fastq.gz	Fastqsanger.gz
	SRR8551171_1.fastq.gz	Fastqsanger.gz

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

Project description: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 (Lin–SCA1+cKIT+(LSK) CD150+ CD48– for HSCs, Lin–SCA1+cKIT+(LSK) CD150– CD48– for MPPs and Lin–SCA1+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.

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Project description:Here we identify the genome-wide occupancy of PHF6 in T-ALL cells. Human T-ALL cells were cross-linked with formaldehyde for 20 min. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against total PHF6 (Bethyl A301-451A). This represents the ChIP-seq portion of this dataset.

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