DOI: 10.6084/m9.figshare.28473866
title: PEtracer Data

description: Processed data accompanying the "High-resolution spatial mapping of cell state and lineage dynamics <i>in vivo</i> with PEtracer" manuscript. Code for generating these files can found on GitHub. H5td files containing single-cell transcriptomics and lineage data can be loaded using TreeData and GeoJSON files contain polygons representing cell outlines can be loaded using GeoPandas.Files:<b>4T1_kinetics.h5ad </b>- 10x single-cell transcriptomic and lineage data for 4T1 cells transduced with a library of pegRNA variants to test their editing kinetics.<b>4T1_kinetics_cells.csv </b>- Cell metadata for cells in 4T1_kinetics.h5ad.<b>4T1_kinetics_alleles.csv </b>- PEtracer allele table for cells in 4T1_kinetics.h5ad.<b>B16F10_kinetics.h5ad </b>- 10x single-cell transcriptomic and lineage data for B16 cells transduced with a library of pegRNA variants to test their editing kinetics.<b>B16F10</b><b>_kinetics_cells.csv </b>- Cell metadata for cells in 4T1_kinetics.h5ad.<b>B16F10</b><b>_kinetics_alleles.csv </b>- PEtracer allele table for cells in 4T1_kinetics.h5ad.<b>preedited_10x_invitro.h5ad </b>- 10x single-cell transcriptomic and lineage data for preedited cells with a known linkage between intBCs and LMs.<b>preedited_10x_invitro_alleles.csv</b> - PEtracer allele table for cells in preedited_10x_invitro.h5ad.<b>preedited_merfish_invitro_cells.json </b>- Spatially resolved lineage data for preedited cells with a known linkage between intBCs and LMs seeded onto a coverslip.<b>preedited_merfish_invitro_alleles.csv </b>- PEtracer allele table for cells in preedited_merfish_invitro_cells.json.<b>preedited_merfish_zombie_cells.json </b>- Spatially resolved lineage data using the zombie protocol for preedited cells with a known linkage between intBCs and LMs seeded onto a coverslip.<b>preedited_merfish_zombie_alleles.csv </b>- PEtracer allele table for cells in preedited_merfish_zombie_cells.json.<b>preedited_merfish_invivo_cells.json </b>- Spatially resolved lineage data for preedited cells with a known linkage between intBCs and LMs from a tumor in the flank of a mouse.<b>preedited_merfish_</b><b>invivo</b><b>_alleles.csv </b>- PEtracer allele table for cells in preedited_merfish_invivo_cells.json.<b>barcoded_tracing_clone_#.h5td</b> - 10x single-cell transcriptomic and lineage data for six clones with puro and blast-linked barcodes serving as independent marks of phylogenetically related cells.<b>barcoded_tracing_alleles.h5td </b>- PEtracer allele table used to reconstruct phylogenies for cells in barcoded_tracing_clone_#.h5td. File includes all six clones.<b>colony_tracing.h5td</b> - Spatially resolved lineage tracing data for 18,675 cells representing 64 clones sparely seeded onto a cover slip.<b>colony</b><b>_polygons.json </b>- Nuclei outlines for cells in colony_tracing.h5td<b>10x_4T1_primary.h5ad</b> - 10x transcriptomic data for 34,141 cells from the lung, liver, and primary 4T1 tumor in the flank of a mouse.<b>4T1_invitro.h5ad</b> - 10x transcriptomic data for 21,644 in vitro cells engineered with the PEtracer components.<b>M1_tumor_tracing.h5td</b> - Spatially resolved transciptomic and lineage data for 262,062 cells from four section of a mouse lung containing 4T1 tumors.<b>M2_tumor_tracing.h5td </b>- Same as above with 106,660 cells from one section.<b>M3_tumor_tracing.h5td </b>- Same as above with 145,954 cells from four section.<b>M1_polygons_grid.json </b>- Nuclei outlines arranged as a grid for cells in M1_tumor_tracing.h5td<b>M2_polygons.json </b>- Nuclei outlines for cells in M2_tumor_tracing.h5td<b>M3_polygons_grid.json </b>- Nuclei outlines arranged as a grid for cells in M3_tumor_tracing.h5td<br><br><br>