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Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars

A key goal of developmental biology is to understand how a single cell is transformed into a full-grown organism comprising many different cell types. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of ce... Full description

Journal Title: Nature biotechnology 2018, Vol.36 (5), p.469-473
Main Author: Spanjaard, Bastiaan
Other Authors: Hu, Bo , Mitic, Nina , Olivares-Chauvet, Pedro , Janjuha, Sharan , Ninov, Nikolay , Junker, Jan Philipp
Format: Electronic Article Electronic Article
Language: English
Subjects:
RNA
Publisher: United States: Nature Publishing Group
ID: ISSN: 1087-0156
Link: https://www.ncbi.nlm.nih.gov/pubmed/29644996
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title: Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars
format: Article
creator:
  • Spanjaard, Bastiaan
  • Hu, Bo
  • Mitic, Nina
  • Olivares-Chauvet, Pedro
  • Janjuha, Sharan
  • Ninov, Nikolay
  • Junker, Jan Philipp
subjects:
  • Animals
  • Bar codes
  • Cancer Research
  • Cell Lineage - genetics
  • Cell Tracking - methods
  • Computational Biology - methods
  • Computer applications
  • CRISPR
  • CRISPR-Cas Systems - genetics
  • Developmental biology
  • DNA sequencing
  • Editing
  • Gene Editing
  • Gene expression
  • Gene sequencing
  • Genetic Engineering
  • Genomes
  • Heart - growth & development
  • High-Throughput Nucleotide Sequencing - methods
  • Larvae
  • Liver
  • Liver - growth & development
  • Liver - metabolism
  • Methods
  • Nuclease
  • Nucleotide sequencing
  • Pancreas
  • Pancreas - growth & development
  • Pancreas - metabolism
  • Ribonucleic acid
  • RNA
  • Scars
  • Single-Cell Analysis - methods
  • Taxonomy
  • Telencephalon
  • Telencephalon - growth & development
  • Telencephalon - metabolism
  • Transcriptome - genetics
  • Transgenic
  • Trees
  • Zebrafish
  • Zebrafish - genetics
  • Zebrafish - growth & development
  • Zebrafish - metabolism
ispartof: Nature biotechnology, 2018, Vol.36 (5), p.469-473
description: A key goal of developmental biology is to understand how a single cell is transformed into a full-grown organism comprising many different cell types. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of cell types into lineage trees to understand the developmental origin of cells remains challenging. Here we present LINNAEUS (lineage tracing by nuclease-activated editing of ubiquitous sequences)-a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae, and in heart, liver, pancreas, and telencephalon of adult fish. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.
language: eng
source:
identifier: ISSN: 1087-0156
fulltext: no_fulltext
issn:
  • 1087-0156
  • 1546-1696
url: Link


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titleSimultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars
creatorSpanjaard, Bastiaan ; Hu, Bo ; Mitic, Nina ; Olivares-Chauvet, Pedro ; Janjuha, Sharan ; Ninov, Nikolay ; Junker, Jan Philipp
creatorcontribSpanjaard, Bastiaan ; Hu, Bo ; Mitic, Nina ; Olivares-Chauvet, Pedro ; Janjuha, Sharan ; Ninov, Nikolay ; Junker, Jan Philipp
descriptionA key goal of developmental biology is to understand how a single cell is transformed into a full-grown organism comprising many different cell types. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of cell types into lineage trees to understand the developmental origin of cells remains challenging. Here we present LINNAEUS (lineage tracing by nuclease-activated editing of ubiquitous sequences)-a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae, and in heart, liver, pancreas, and telencephalon of adult fish. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.
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languageeng
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subjectAnimals ; Bar codes ; Cancer Research ; Cell Lineage - genetics ; Cell Tracking - methods ; Computational Biology - methods ; Computer applications ; CRISPR ; CRISPR-Cas Systems - genetics ; Developmental biology ; DNA sequencing ; Editing ; Gene Editing ; Gene expression ; Gene sequencing ; Genetic Engineering ; Genomes ; Heart - growth & development ; High-Throughput Nucleotide Sequencing - methods ; Larvae ; Liver ; Liver - growth & development ; Liver - metabolism ; Methods ; Nuclease ; Nucleotide sequencing ; Pancreas ; Pancreas - growth & development ; Pancreas - metabolism ; Ribonucleic acid ; RNA ; Scars ; Single-Cell Analysis - methods ; Taxonomy ; Telencephalon ; Telencephalon - growth & development ; Telencephalon - metabolism ; Transcriptome - genetics ; Transgenic ; Trees ; Zebrafish ; Zebrafish - genetics ; Zebrafish - growth & development ; Zebrafish - metabolism
ispartofNature biotechnology, 2018, Vol.36 (5), p.469-473
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descriptionA key goal of developmental biology is to understand how a single cell is transformed into a full-grown organism comprising many different cell types. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of cell types into lineage trees to understand the developmental origin of cells remains challenging. Here we present LINNAEUS (lineage tracing by nuclease-activated editing of ubiquitous sequences)-a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae, and in heart, liver, pancreas, and telencephalon of adult fish. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.
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abstractA key goal of developmental biology is to understand how a single cell is transformed into a full-grown organism comprising many different cell types. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of cell types into lineage trees to understand the developmental origin of cells remains challenging. Here we present LINNAEUS (lineage tracing by nuclease-activated editing of ubiquitous sequences)-a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae, and in heart, liver, pancreas, and telencephalon of adult fish. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.
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