Single-cell RNA-seq analysis of cardiac gastruloids for Rossi et al. Cell Stem Cell 2020.
Download the data from GEO, install R-studio and Seurat v3, and use the file Explore_Data.R for a quick dive into cell annotations and gene expression, and to be setup for further exploration in R.
To reproduce the complete analysis, obtain the raw data from Rossi et al. 2020 (cardiac gastruloids, fastq files on SRA) as well as Pijuan-Sala et al. 2019 (used as a reference in vivo atlas). Install all dependencies listed in SessionInfo.txt, download the input tables, cell-type classifier, and complete code, and run cellranger for alignment, velocyto for RNA splicing estimates, followed by CardiacGastruloidsAnalysis.R for the main analysis, and by the jupyter lab notebooks for RNA-velocity calculations with scVelo.