Project description:Purpose: The study was designed to identify transcriptional differences of P0 liver HSCs with different genotypes or different cell size. Method: For RNA-seq, libraries were prepared according to the Smart-seq2 protocol from 100-200 sorted HSCs. Samples were sequenced by NextSeq500 (Illumina) with single-end 75-bp read length using the NextSeq 500/550 High Output v2 Kit (75 cycles, Illumina). The RNA-seq pipeline from Basepair (www.basepairtech.com) was used for the analysis. Expression count was analyzed by STAR and differential expression by DESeq2 (P < 0.05 and fold-change > 2).
Project description:Hepatic stellate cells are the primary cell type responsible for development of fibrosis in chronic liver disease. We used directional RNA sequencing (RNA-seq) and chromatin immunoprecipitation and sequencing (ChIP-seq) to identify the lncRNAs expressed in human HSCs. We also identified the lncRNAs that change in expression with differentiation of nonfibrotic quiescent HSCs into fibrotic HSC myofibroblasts and those that are regulated by TGF-beta signaling. ChIP-seq was also performed to identify DNA regions occupied by H3K27ac to define super-enhancers in HSC myofibroblasts. This study identified lncRNAs expressed HSCs that may regulate fibrosis. Analysis of genome-wide lncRNA expression using RNA-seq and ChiP-seq in human HSCs under four different conditions
Project description:To gain insight into the differential expressed genes in immune edited tumor cell lines, we performed genome-wide RNA-sequencing analysis (RNA-seq) in parental P0 (CaSki-P0) and immune edited P3 (CaSki-P3) cells.
Project description:we utilize Nano-MeDIP-seq for the analysis of the LT-HSC methylome and, for the first time, simultaneously interrogate the methylome and transcriptome of a homogeneous population of primary murine HSCs, in order to define the underlying causes of changes in HSC functionality during normal ageing. We isolated and phenotyped primary LT-HSCs from young, middle-aged and old mice and subjected them to comprehensive methylome (MeDIP-seq) and transcriptome (RNA-seq) analysis.
Project description:We present a transcriptomic atlas of spinal V1 interneurons across postnatal development (P0, P14, P28, and P56) in the mouse using single-nucleus RNA sequencing (snRNA-seq). We also present transcriptomic data comparing V1 interneurons in En1 heterozygous and En1 KO mice at age P0 only.