RNAseq of LSEC from WT and Bmp9-KO mice in 129/Ola genetic background. 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得到25周龄雌性小鼠的肝窦内皮细胞（Liver Sinusoidal Endothelial Cells, LSEC），并对野生型（Wild Type, WT）及Bmp9基因敲除（Bmp9 knockout, Bmp9-KO）的LSEC样本开展批量转录组测序。本研究旨在对比WT与Bmp9-KO样本间的差异生物学过程，因已知BMP9是由肝星状细胞（hepatic stellate cells）分泌的血管静息因子。测序读段经Trimmomatic v.0.36（文献16）质控修剪，以去除潜在接头序列及低质量碱基；随后使用STAR比对工具v.2.5.2b（文献17）将修剪后的读段比对至ENSEMBL数据库发布的小鼠（Mus musculus）MM10参考基因组。采用Subread软件包v.1.5.2中的"featureCounts"工具计算唯一基因比对计数。本研究的野生型样本为F126、F121、F120、F119、F135，基因敲除型样本为F131、F132、F124及F133。