Code for cardio scRNA-seq analysis and figure plots from manuscript A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes.

Overview: Manuscript data set contains single cell RNA-sequencing data from in vitro hiPSC derived cardiomyocytes and includes both raw (fastq) and processed data (count matrix).

Cardiomyocyte differentiation and sample collection

hiPSCs were differentiated into cardiomyocytes using two protocols: small molecule (Lian et al. 2012) and cytokine (Palpant et al. 2015). Samples were collected for sequencing at 4 time points: 1) D0 time point before the initiation of differentiation, 2) D12/D14 after differentiation was initiated, 3) D24/D26, and 4) D90.

Library preparation and sequencing

Single cell libraries were prepared using the Split-Seq method. (see manuscript for more details)