Building a lineage from single cells: genetic techniques for cell lineage tracking.
Mollie B. Woodworth,Kelly M. Girskis,Kelly M. Girskis,Kelly M. Girskis,Christopher A. Walsh,Christopher A. Walsh,Christopher A. Walsh +6 more
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TLDR
A recent explosion of methodological advances in exogenous labelling and single-cell sequencing have enabled lineage tracking at larger scales, in more detail, and in a wider range of species than was previously considered possible.Abstract:
Lineage analyses of multicellular organisms provide key insights into developmental mechanisms and how these developmental trajectories go awry in diverse diseases. This Review discusses the features, technical challenges and latest opportunities of an evolving range of sophisticated genetic techniques for tracking cell lineages in organisms. These strategies include methods for prospective tracking using engineered genetic constructs, as well as retrospective tracking based on naturally occurring somatic mutations.read more
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SF-010-4 Distant metastasis occurs late during the genetic evolution of pancreatic cancer
TL;DR: A quantitative analysis of the timing of the genetic evolution of pancreatic cancer was performed, indicating at least a decade between the occurrence of the initiating mutation and the birth of the parental, non-metastatic founder cell.
Journal ArticleDOI
Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation
Jason D. Buenrostro,Jason D. Buenrostro,M. Ryan Corces,Caleb A. Lareau,Caleb A. Lareau,Beijing Wu,Alicia N. Schep,Martin J. Aryee,Martin J. Aryee,Ravindra Majeti,Howard Y. Chang,William J. Greenleaf +11 more
TL;DR: A chromatin accessibility landscape of human hematopoiesis is constructed and variation consistent with lineage bias toward different developmental branches in multipotent cell types is found, providing a framework for integrative exploration of complex regulatory dynamics in a primary human tissue at single-cell resolution.
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Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain.
Bushra Raj,Daniel E. Wagner,Aaron McKenna,Shristi Pandey,Allon M. Klein,Jay Shendure,Jay Shendure,James A. Gagnon,James A. Gagnon,Alexander F. Schier +9 more
TL;DR: ScGESTALT as discussed by the authors combines the lineage recording capabilities of GESTALT with cell-type identification by single-cell RNA sequencing, which relies on an inducible system that enables barcodes to be edited at multiple time points, capturing lineage information from later stages of development.
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Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars
Bastiaan Spanjaard,B. Hu,Nina Mitic,Pedro Olivares-Chauvet,Sharan Janjuha,Nikolay Ninov,Jan Philipp Junker +6 more
TL;DR: LINNAEUS (lineage tracing by nuclease-activated editing of ubiquitous sequences)—a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells for tracing the origin of novel cell types, or known cell types under different conditions.
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Lineage tracing on transcriptional landscapes links state to fate during differentiation
Caleb Weinreb,Alejo E. Rodriguez-Fraticelli,Alejo E. Rodriguez-Fraticelli,Fernando D. Camargo,Fernando D. Camargo,Allon M. Klein +5 more
TL;DR: This work established how variation in transcriptional state biases future cell fate and whether scSeq is sufficient to completely distinguish cells with distinct fate biases and developed a tool called LARRY, which clonally tags cells with DNA barcodes that can be read using scSequ.
References
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Clonally related cortical cells show several migration patterns
TL;DR: This hypothesis that the cortex consists of radial, ontogenetic units of clonally related neurons was tested by studying cell lineage in the rat cortex with a retroviral vector carrying the Escherichia coli beta-galactosidase gene, which can be easily visualized.
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Je-Hyuk Lee,Evan R. Daugharthy,Jonathan Scheiman,Reza Kalhor,Thomas C. Ferrante,Richard C. Terry,Brian M. Turczyk,Joyce L. Yang,Hosuk Lee,John Aach,Kun Zhang,George M. Church +11 more
TL;DR: A protocol for genome-wide profiling of gene expression in situ in fixed cells and tissues, in which RNA is converted into cross-linked cDNA amplicons and sequenced manually on a confocal microscope, which enriches for context-specific transcripts over housekeeping and/or structural RNA.
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Design and Analysis of Single-Cell Sequencing Experiments
TL;DR: This Primer provides an overview of available methods and discusses experimental design and single-cell data analysis and hopes that these guidelines will enable a growing number of researchers to leverage the power of single- cell sequencing.
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Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding
TL;DR: This work demonstrates how to combine viral genetic barcoding with high-throughput sequencing to track the in vivo differentiation of unitary hematopoietic stem cells (HSCs), and suggests that HSCs do not equally contribute to blood cells after irradiation-mediated transplantation.
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Spatially resolved transcriptomics and beyond
TL;DR: Pioneering technologies that enable spatially resolved transcriptomics are summarized and how these methods have the potential to extend beyond transcriptomics to encompass spatially resolution genomics, proteomics and possibly other omic disciplines are discussed.