DOI: 10.5061/dryad.478t9
title: Data from: Whole organism lineage tracing by combinatorial and cumulative genome editing

description: Multicellular systems develop from single cells through distinct lineages.
 However, current lineage-tracing approaches scale poorly to whole, complex
 organisms. Here, we use genome editing to progressively introduce and
 accumulate diverse mutations in a DNA barcode over multiple rounds of cell
 division. The barcode, an array of clustered regularly interspaced short
 palindromic repeats (CRISPR)/Cas9 target sites, marks cells and enables
 the elucidation of lineage relationships via the patterns of mutations
 shared between cells. In cell culture and zebrafish, we show that rates
 and patterns of editing are tunable and that thousands of
 lineage-informative barcode alleles can be generated. By sampling hundreds
 of thousands of cells from individual zebrafish, we find that most cells
 in adult organs derive from relatively few embryonic progenitors. In
 future analyses, genome editing of synthetic target arrays for lineage
 tracing (GESTALT) can be used to generate large-scale maps of cell lineage
 in multicellular systems for normal development and disease.
description: Phylogenetic tree for V6
 30hpf embryo #7A tree created with the
 PHYLIP Mix package from DNA sequenced from a 30hpf zebrafish embryo with
 an integrated GESTALT barcode, exposed to CRISPR/Cas9 editing
 reagents.embryos_1_7.jsonfish_ADR1_PHYLIP_MIX_gte5a maximum parsimony tree of GESTALT barcodes collected from adult zebrafish ADR1. The tree was assembled using the PHYLIP Mix software package and annotated into a JSON data object for visualizationfish_ADR2_PHYLIP_MIX_gt5a maximum parsimony tree of GESTALT barcodes collected from adult zebrafish ADR2. The tree was assembled using the PHYLIP Mix software package and annotated into a JSON data object for visualizationcell_culture_gte2a maximum parsimony tree of GESTALT barcodes collected from cell culture lineages. The tree was assembled using the PHYLIP Mix software package and annotated into a JSON data object for visualizationembryos_1_7the raw maximum parsimony tree set output of GESTALT barcodes collected from embryo #7, a 30hpf zebrafish embryo. The file contains the all of the raw PHYLIP Mix software package output treesfish_ADR2_PHYLIP_MIX_gte5_outputthe raw maximum parsimony tree set output of GESTALT barcodes collected from adult zebrafish ADR2. The file contains the all of the raw PHYLIP Mix software package output treesfish_ADR1_PHYLIP_MIX_gte5_outputthe raw maximum parsimony tree set output of GESTALT barcodes collected from adult zebrafish ADR1. The file contains the all of the raw PHYLIP Mix software package output treescell_culture_gte2_MIX_outputthe raw maximum parsimony tree set output of GESTALT barcodes collected from a cell culture lineage simulation. The file contains the all of the raw PHYLIP Mix software package output treesall_stats_files.tarcontains all the UMI and read alignments used to produce the associated treesembryos_1_7 data matrixdata matrix input to PHYLIP Mix for embryo #7, a v6 30hpf embryoembryos_1_7.mixfish_ADR2_PHYLIP_MIX_gte5_input data matrixthe data matrix for adult fish ADR2, used as input to PHYLIP Mixfish_ADR2_PHYLIP_MIX_gte5_input.txtfish_ADR1_PHYLIP_MIX_gte5_inputthe data matrix for adult fish ADR1, used as input to PHYLIP Mixcell_culture_gte2_input_MIXthe data matrix for the cell culture experiment, used as input to PHYLIP MixNCBI accession GSE81713All raw fastq data files, and post-processed read files for all samples.