2.4. Gene Expression Heterogeneity Analyses
All short reads were mapped to the CHO K1 RefSeq assembly (22,516 sequences, RefSeq Assembly ID: GCF_000223135.1) and CHO K1 mitochondrial DNA (1 sequence, RefSeq Assembly ID: GCF_000055695.1) using Bowtie2 v. 2.3.0 (Langmead, Wilks, Antonescu, & Charles, 2018). Estimating gene and isoform expression levels from the RNA-Seq data was performed with RSEM v. 1.2.31 (B. Li & Dewey, 2011). Principal component analyses (PCA) of the single-cell RNA-seq data were performed with R v. 3.0.1 and the R Stats Package v. 3.2.2 (RCoreTeam, 2013). The Bartlett test for the homogeneity of variances in principal components 1 between different culture times (Days) was performed with the R Stats Package v. 3.2.2.