RNAseq of LSEC from WT and Bmp9-KO mice in 129/Ola genetic background

LSEC fom WT and Bmp9-KO 25-weeks female mice were isolated using collagenase and treated for bulk RNAsequencing. The objective was to determine the biological processes that are altered in Bmp9-KO compared to WT, as BMP9 is know to be a vascular quiescence factor produced by hepatic stellate cells. RNAseq reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36 16. The trimmed reads were mapped to the Mus Musculus MM10 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b 17. Unique gene hit counts were calculated by using 'featureCounts' from the Subread package v.1.5.2 WT samples are F126, F121, F120, F119, F135 KO samples are F131, F132, F124 and F133本研究采用胶原酶分离25周龄雌性野生型（Wild Type, WT）与骨形态发生蛋白9基因敲除（Bmp9-KO）小鼠的肝窦内皮细胞（LSEC），并开展批量RNA测序（bulk RNA sequencing）。本研究旨在明确相较于野生型小鼠，Bmp9-KO小鼠体内发生异常改变的生物学过程——已知骨形态发生蛋白9（BMP9）是由肝星状细胞分泌的血管静息因子。测序所得的RNA读段经Trimmomatic v.0.36 16进行质控修剪，以去除潜在的接头序列与低质量碱基；随后利用STAR比对工具v.2.5.2b 17，将修剪后的读段比对至ENSEMBL数据库发布的小家鼠（Mus musculus）MM10参考基因组。通过Subread软件包v.1.5.2中的"featureCounts"工具计算唯一基因比对计数。野生型样本包括F126、F121、F120、F119、F135；基因敲除型样本包括F131、F132、F124及F133。