title: Transcriptional profiling of the epigenetic regulator Smchd1.
abstract: Smchd1 is an epigenetic repressor with important functions in healthy cellular processes and disease. To elucidate its role in transcriptional regulation, we performed two independent genome-wide RNA-sequencing studies comparing wild-type and Smchd1 null samples in neural stem cells and lymphoma cell lines. Using an R-based analysis pipeline that accommodates observational and sample-specific weights in the linear modeling, we identify key genes dysregulated by Smchd1 deletion such as clustered protocadherins in the neural stem cells and imprinted genes in both experiments. Here we provide a detailed description of this analysis, from quality control to read mapping and differential expression analysis. These data sets are publicly available from the Gene Expression Omnibus database (accession numbers GSE64099 and GSE65747).
authors.affiliation: Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.
authors.forename: Ruijie
authors.initials: R
authors.lastname: Liu
authors.affiliation: Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia.
authors.forename: Kelan
authors.initials: K
authors.lastname: Chen
authors.affiliation: Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia.
authors.forename: Natasha
authors.initials: N
authors.lastname: Jansz
authors.affiliation: Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia.
authors.forename: Marnie E
authors.initials: ME
authors.lastname: Blewitt
authors.affiliation: Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia; School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia.
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Ritchie
keywords: Epigenetics; RNA-sequencing; Sample variability; voom