Sequencing of Cardiomyocyte and Non-Cardiomyocyte Transcriptomes

To validate our in vitro sequencing in tissue, cardiomyocytes and non-cardiomyocytes were isolated from 8-week-old male wild-type C57BL/6 mice as described previously by Trembinski et al. [29 (link)]. Briefly, cardiomyocytes were separated from other cells, such as fibroblasts and ECs, via density centrifugation. RNA isolation was done using the RNeasy Mini Kit and the RNase-Free DNase Set (Qiagen). RNA sequencing was performed as described previously [30 (link)]. Briefly, poly-A RNA was selected using poly-T oligo attached beads. Sequencing libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) and sequencing was done using the HiSeq 2000 flowcell (Illumina). Reads were mapped using TopHat (2 mismatches) and gene expression was estimated using Cufflinks version 2.1 with default parameters.