title: MIWT-Control-2
design: Cells were harvested for RNA extraction at 10000 g, 4 C, for 10 min. Procedures for RNA extraction, RNA enrichment and preparation of DNA library for sequencing using Illumina HiSeq were carried out as described in Khan, et al 2017 (PMID: 28729683).  Following sequence run, a pair of FASTQ files were derived from each sample. For differential expression analysis of genes, raw read counts for the S. mitis type strain and SK321 transcripts were generated using a Perl script based on the mapped read profiles of the two strains. The DESeq Bioconductor software package was used for assessment of differential expression levels when comparing samples.