Processed data for KP-Tracer Tumors from study "Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution"

This repository contains processed data associated with the manuscript "Lineage Recording Reveals the Phylodynamics, Plasticity, and Paths of Tumor Evolution" (Yang*, Jones*, et al bioRxiv 2021). In this study, single-cell lineage tracing was performed in the KP autochthonous mouse model of non-small-cell lung cancer. Tumors were initiated with Cre recombinase (and optionally an additional gRNA targeting the other well-studied tumor suppressors) and allowed to grow for approximately 4-6 months at which point mice were sacrificed and tumors harvested. After purifying cancer cells by fluorescent markers, cells were profiled with the 10X chromium platform and four libraries were collected: a single-cell transcriptome library, a single-cell lineage tracing library, a single-cell multiplexing library, and a single-cell lenti-barcode library (used for confirming the clonality of tumors). Data was processed using the 10X Cellranger suite and custom pipelines as described in the manuscript above. Data here represents the derived processed data from our analysis. The specific contents are described in a README contained within the repository. Briefly, however, we have provided here processed AnnData objects for the KP data (sgNT) and the integrated data across three genotypes (KP, KPA, and KPL). We also provide the gene lists associated with fitness, expansion annotations for each tree, as well as plasticity scores amongst other items. For code used in this study, we additionally have provided a reproducibility repository at https://github.com/mattjones315/KPTracer-release