PEtracer Data

Processed data accompanying the "High-resolution spatial mapping of cell state and lineage dynamics in vivo 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:4T1_kinetics.h5ad - 10x single-cell transcriptomic and lineage data for 4T1 cells transduced with a library of pegRNA variants to test their editing kinetics.
4T1_kinetics_cells.csv - Cell metadata for cells in 4T1_kinetics.h5ad.
4T1_kinetics_alleles.csv - PEtracer allele table for cells in 4T1_kinetics.h5ad.
B16F10_kinetics.h5ad - 10x single-cell transcriptomic and lineage data for B16 cells transduced with a library of pegRNA variants to test their editing kinetics.
B16F10_kinetics_cells.csv - Cell metadata for cells in 4T1_kinetics.h5ad.
B16F10_kinetics_alleles.csv - PEtracer allele table for cells in 4T1_kinetics.h5ad.
preedited_10x_invitro.h5ad - 10x single-cell transcriptomic and lineage data for preedited cells with a known linkage between intBCs and LMs.
preedited_10x_invitro_alleles.csv - PEtracer allele table for cells in preedited_10x_invitro.h5ad.
preedited_merfish_invitro_cells.json - Spatially resolved lineage data for preedited cells with a known linkage between intBCs and LMs seeded onto a coverslip.
preedited_merfish_invitro_alleles.csv - PEtracer allele table for cells in preedited_merfish_invitro_cells.json.
preedited_merfish_zombie_cells.json - Spatially resolved lineage data using the zombie protocol for preedited cells with a known linkage between intBCs and LMs seeded onto a coverslip.
preedited_merfish_zombie_alleles.csv - PEtracer allele table for cells in preedited_merfish_zombie_cells.json.
preedited_merfish_invivo_cells.json - Spatially resolved lineage data for preedited cells with a known linkage between intBCs and LMs from a tumor in the flank of a mouse.
preedited_merfish_invivo_alleles.csv - PEtracer allele table for cells in preedited_merfish_invivo_cells.json.
barcoded_tracing_clone_#.h5td - 10x single-cell transcriptomic and lineage data for six clones with puro and blast-linked barcodes serving as independent marks of phylogenetically related cells.
barcoded_tracing_alleles.h5td - PEtracer allele table used to reconstruct phylogenies for cells in barcoded_tracing_clone_#.h5td. File includes all six clones.
colony_tracing.h5td - Spatially resolved lineage tracing data for 18,675 cells representing 64 clones sparely seeded onto a cover slip.
colony_polygons.json - Nuclei outlines for cells in colony_tracing.h5td
10x_4T1_primary.h5ad - 10x transcriptomic data for 34,141 cells from the lung, liver, and primary 4T1 tumor in the flank of a mouse.
4T1_invitro.h5ad - 10x transcriptomic data for 21,644 in vitro cells engineered with the PEtracer components.
M1_tumor_tracing.h5td - Spatially resolved transciptomic and lineage data for 262,062 cells from four section of a mouse lung containing 4T1 tumors.
M2_tumor_tracing.h5td - Same as above with 106,660 cells from one section.
M3_tumor_tracing.h5td - Same as above with 145,954 cells from four section.
M1_polygons_grid.json - Nuclei outlines arranged as a grid for cells in M1_tumor_tracing.h5td
M2_polygons.json - Nuclei outlines for cells in M2_tumor_tracing.h5td
M3_polygons_grid.json - Nuclei outlines arranged as a grid for cells in M3_tumor_tracing.h5td