RIN is a standard measure of RNA quality, but it focuses on the integrity of ribosomal RNA, rather than surveying quality of RNA from genes throughout the genome. A few alternatives to RIN have been proposed, a very recent proposal being the “mRIN” method65, which analyzes read coverage over transcripts and derives statistics related to quality. Here we use the mRIN software to evaluate the RNA quality of the samples. The CMC data were processed using the pipeline described on the mRIN website (http://zhanglab.c2b2.columbia.edu/index.php/MRIN). Parameters were set as suggested in the documentation. Additional filtering based on gene expression values was not performed. Data were analyzed without any QC beyond what is automatically implemented in mRIN.
