Analysis of Kinkel (C086) Smchd1 LSK mini-bulk data set

Peter Hickey https://peterhickey.org (Single Cell Open Research Endeavour (SCORE), WEHI)https://www.wehi.edu.au/people/shalin-naik/3310/score
2021-10-15

Overview

In this analysis, we analysis mini-bulk data of LSKs from mice with various Smcd1 genotypes looking for differential expression between Del and Het mice.

After sequencing, expression was quantified by counting the number of UMIs mapped to each gene using scPipe(Tian et al. 2018). Count data for all endogeneous genes (GENCODE Release 28 (GRCm38.p6)) and spike-in transcripts (ERCC) are available in this repository.

This analysis is adapted from RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR workflow (Law et al. 2016).

Analysis version information

R version: R version 4.0.3 (2020-10-10)

Bioconductor version: 3.12

Law, Charity W, Monther Alhamdoosh, Shian Su, Xueyi Dong, Luyi Tian, Gordon K Smyth, and Matthew E Ritchie. 2016. “RNA-Seq Analysis Is Easy as 1-2-3 with Limma, Glimma and edgeR.” F1000Research 5.
Tian, Luyi, Shian Su, Xueyi Dong, Daniela Amann-Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J Hilton, Shalin H Naik, and Matthew E Ritchie. 2018. “scPipe: A Flexible r/Bioconductor Preprocessing Pipeline for Single-Cell RNA-Sequencing Data.” PLoS Computational Biology 14 (8): e1006361. https://www.ncbi.nlm.nih.gov/pubmed/30096152.

References