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.
Phylogenetic tree for V6 30hpf embryo #7
A 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.json
fish_ADR1_PHYLIP_MIX_gte5
a 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 visualization
fish_ADR2_PHYLIP_MIX_gt5
a 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 visualization
cell_culture_gte2
a 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 visualization
embryos_1_7
the 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 trees
fish_ADR2_PHYLIP_MIX_gte5_output
the 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 trees
fish_ADR1_PHYLIP_MIX_gte5_output
the 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 trees
cell_culture_gte2_MIX_output
the 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 trees
all_stats_files.tar
contains all the UMI and read alignments used to produce the associated trees
embryos_1_7 data matrix
data matrix input to PHYLIP Mix for embryo #7, a v6 30hpf embryo
embryos_1_7.mix
fish_ADR2_PHYLIP_MIX_gte5_input data matrix
the data matrix for adult fish ADR2, used as input to PHYLIP Mix
fish_ADR2_PHYLIP_MIX_gte5_input.txt
fish_ADR1_PHYLIP_MIX_gte5_input
the data matrix for adult fish ADR1, used as input to PHYLIP Mix
cell_culture_gte2_input_MIX
the data matrix for the cell culture experiment, used as input to PHYLIP Mix
NCBI accession GSE81713
All raw fastq data files, and post-processed read files for all samples.