RNAseq analysis in Dnmt3a LSK cells from mice with expansion vs mice with no expansion in mosaic mice infected with M. avium

15000 CD45.2 LSK from 3 individual recipient mice (mosaic mice) that showed clear Dnmt3a-/-clonal expansion at the end of the 2-month M. avium infection and 2 individual recipient mice without Dnmt3a-/-clonal expansion at the end of the 2-month M. avium infection. RNA was isolated with the NucleoSpin ® RNA Plus XS kit (Macherey Nagel). RNA-seq libraries were prepared by using SMARTer® Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (Takara Bio Usa). Illumina NovaSeq SP was used for sequencing with a paired-end sequencing length of 10bp. Following steps were taken to analyze the data:

1. Alignment of RNA-Seq reads with the STAR aligner
2. Assignment of aligned reads to genes
3. Differential gene expression with DESeq2