Pluto Bioinformatics

GSE65747: Genome-wide binding and mechanistic analyses of Smchd1 mediated epigenetic regulation [RNA-Seq]

Bulk RNA sequencing

Purpose: The aim of this study is to identify genes that are under the transcriptional control of the epigenetic regulator Smchd1 in neural stem cells (NSCs) derived from E14.5 mouse brain; Methods: Total RNA was extracted using an AllPrep DNA/RNA Mini Kit (Qiagen) from cultured neural stem cells derived from male mouse E14.5 brains either wild-type or null for Smchd1. 1 g total RNA was used to generate sequencing libraries for whole transcriptome analysis with Illuminas TruSeq RNA Sample Preparation Kit v2 as per standard protocols. Libraries were sequenced on HiSeq 2000 with Illumina TruSeq SBS Kit v3-HS reagents as either 100 bp single-end or paired-end reads at the Australian Genome Research Facility (AGRF), Melbourne. Reads were aligned to the mouse reference genome mm10 and mapped to known genomic features at the gene level using the Rsubread package (version 1.10.5) (Liao et al. 2013). Mapped reads were then summarized into gene-level counts using FeatureCounts (Liao et al. 2014). SOURCE: Ruijie Liu (cliu@wehi.edu.au) - Ritchie lab walter and eliza hall institute of medical research