GSE201475
R274X mutation in Phf6 enhances self-renewal and repopulation capacity of hematopoietic stem cells
Purpose: Next-generation sequencing (NSG) has revolutionized system-based analysis of cellular pathways. The goals of this study are to compare Phf6R274X mice BM LSK cells transcription profiling (RNA-seq)  Method: BM LSK cells mRNA profiles of Phf6R274X mice and control were generated by deep sequencing, in triplicate, using illumine GAIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.  Results: Using an optimized data analysis workflow, we identified 613 genes up-regulated and 133 genes down-regulated (P < 0.05) in the BM LSK cells from Phf6R274X and control mice. Altered expression of 7 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes may contribute to analyze PHF6R274X mutation function.  Conclusion: Our study represents the first detailed analysis of BM LSK cell transcriptomes with PHF6R274X mutation. Our results suggested that Phf6R274X mutation enhanced the regeneration capacity of hematopoietic cells mainly by promoting the activity of cell proliferation and differentiation-related signaling pathways. Overall design: BM LSK cells from  Phf6R274X mouse model and controls .