Data from: Whole organism lineage tracing by combinatorial and cumulative genome editing

McKenna A, Findlay GM, Gagnon JA, Horwitz MS, Schier AF, Shendure J

Date Published: May 26, 2016

DOI: http://dx.doi.org/10.5061/dryad.478t9

 

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Title Phylogenetic tree for V6 30hpf embryo #7
Downloaded 22 times
Description 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.
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Title fish_ADR1_PHYLIP_MIX_gte5
Downloaded 7 times
Description 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
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Title fish_ADR2_PHYLIP_MIX_gt5
Downloaded 5 times
Description 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
Download fish_ADR2_PHYLIP_MIX_gt5.json (232.8 Kb)
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Title cell_culture_gte2
Downloaded 9 times
Description 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
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Title embryos_1_7
Downloaded 14 times
Description 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
Download embryos_1_7.newick (961.7 Kb)
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Title fish_ADR2_PHYLIP_MIX_gte5_output
Downloaded 4 times
Description 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
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Title fish_ADR1_PHYLIP_MIX_gte5_output
Downloaded 5 times
Description 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
Download fish_ADR1_PHYLIP_MIX_gte5_output.newick (440.9 Kb)
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Title cell_culture_gte2_MIX_output
Downloaded 5 times
Description 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
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Title all_stats_files.tar
Downloaded 11 times
Description contains all the UMI and read alignments used to produce the associated trees
Download all_stats_files.tar.bz2 (66.03 Mb)
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Title embryos_1_7 data matrix
Downloaded 8 times
Description data matrix input to PHYLIP Mix for embryo #7, a v6 30hpf embryo
Download embryos_1_7.mix (1.795 Mb)
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Title fish_ADR2_PHYLIP_MIX_gte5_input data matrix
Downloaded 8 times
Description the data matrix for adult fish ADR2, used as input to PHYLIP Mix
Download fish_ADR2_PHYLIP_MIX_gte5_input.txt (629.6 Kb)
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Title fish_ADR1_PHYLIP_MIX_gte5_input
Downloaded 8 times
Description the data matrix for adult fish ADR1, used as input to PHYLIP Mix
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Title cell_culture_gte2_input_MIX
Downloaded 10 times
Description the data matrix for the cell culture experiment, used as input to PHYLIP Mix
Download cell_culture_gte2_input_MIX.txt (50.51 Kb)
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Title NCBI accession GSE81713
Description All raw fastq data files, and post-processed read files for all samples.
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When using this data, please cite the original publication:

McKenna A, Findlay GM, Gagnon JA, Horwitz MS, Schier AF, Shendure J (2016) Whole organism lineage tracing by combinatorial and cumulative genome editing. Science 353(6298): 462. http://dx.doi.org/10.1126/science.aaf7907

Additionally, please cite the Dryad data package:

McKenna A, Findlay GM, Gagnon JA, Horwitz MS, Schier AF, Shendure J (2016) Data from: Whole organism lineage tracing by combinatorial and cumulative genome editing. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.478t9
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