GSE160525
Quantitative Analysis by Next Generation Sequencing of LSK (Lin- Sca1+ cKit+) hematopoietic progenitors transcriptomes from wild type and Usp15-/- mice.
Purpose: the goal of this study is to investigate the consequences of ubiquitin specific protease 15 (USP15) deletion on gene expression in mouse LSK hematopoietic progenitors. Methods: mRNA profiles of 8 weeks-old wild-type (WT) and ubiquitin specific protease 15  knockout (Usp15-/-) mice were generated by deep sequencing using Illumina Hiseq2500. The sequence reads that passed quality filters  Alignments of the sequence reads that passed quality filters were performed using TopHat2.1, Genome build 38 and Ensembl gtf version 77 and genecounts have been generated using Itreecount. https://github.com/NKI-GCF/itreecount Results: We assigned about 30 million reads per sample uniquely to a gene of the mouse reference genome (mm10) We identified 21,219 genes in the LSKs  of WT and Usp15-/- mice using TopHat2.1 in combination with Itreecount. https://github.com/NKI-GCF/itreecount. Distinct LSK-specific expressed genes (such as Eng, Tek, the MlI receptor and the Kit receptor) are identified.  Comparison of normalized gene expression data for Usp15-/- versus WT LSK confirmed the loss of Usp15. Apart from Usp15, almost no other significantly deregurated genes were detected using a treshold of fold change =1.5 and p value <0.05, suggesting the maintenance of an overall stable identity of the cellular compartment in Usp15-/- mice. Conclusions: Our results represent the first detailed analyis of the consequences of USP15 deletion on gene expression in hematopoietic populations such as LSKs progenitors by genome wide expression profiling in WT and Usp15-/- mice. RNAseq of two freshly isolated biological replicas of sorted LSKs from 8 weeks old Usp15-/- animals confirmed the loss of Usp15, while showing almost no significant other up or down regulated genes among the 21,219 genes identified in Usp15-/- LSKs.  We conclude that young adult hematopoietic stem and progenitor cells (LSKs) perpetuated a stable gene expression program regardless of the homozygous deletion of USP15. Overall design: mRNA profiles of 8 weeks-old wild type (WT) and Usp15-/- mice were generated by deep sequencing using Illumina Hiseq2500.  WT n=3, Usp15-/- n=2 mice were analized. FACS sorted LSK (Lin- Sca1+ cKit+) cells freshly isolated from the bone marrow of individual animals were subjected to deep sequencing.