scRNA Seq Preprocessing

All samples were processed using single-cell pipelines in Cumulus that were run through the Terra cloud platform environment. We used Cumulus to carry out both data pre-processing (raw sequencing data to gene expression matrices) and analysis (gene expression matrices to cell type identification), and full documentation is available here.

Full-length transcriptome scRNA-Seq data (SMART-Seq2) was processed to gene expression matrices using bcl2fastq and the SMART-Seq2 workflow documented here.

3'-scRNA-Seq data (10x) was processed to count matrices using the cellranger workflow documented here.