Mouse Smartseq3 Data from Mold et al. Clonally Heritable Gene Expression Imparts a Layer of Diversity in Cell Types

Mouse cells harvested from the central nervous system of two different mice injected at post-coital day 9.5 with lentivirus encoding barcodes that allow for clonal tracking and gene expression in single cell RNAseq measurements (TREX, Ratz et al 2022). Cells are isolated from the cortex 14 days after birth and profiled by scRNA-seq using the Smartseq3 method. Smartseq3 libraries were prepared on single cells isolated from the mouse cortex and FACS sorted based on GFP expression (indicating lentiviral expression of clonal barcodes) according to the standard protocol (https://www.protocols.io/view/smart-seq3-protocol-36wgq5rjxgk5/v3). Please note that Series supplementary files include an example of how the .yaml file for the zumis-run looks like, the expected barcodes and the .fa file for lentiviral barcodes within the samples, which are needed to accurately regenerate the entire pipeline.