Recent advances in lineage tracing for the kidney

Lineage Tracing.

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Lineage-tracing methods and the kidney.

Kidney International. 2014; 86: 481-488

The CRISPR tool kit for genome editing and beyond.

Nat Commun. 2018; 9: 1911

The promise of single-cell RNA sequencing for kidney disease investigation.

Kidney International. 2017; 92: 1334-1342

Functional expression of the cre-lox site-specific recombination system in the yeast Saccharomyces cerevisiae.

Mol Cell Biol. 1987; 7: 2087-2096

Conditional control of gene expression in the mouse.

Nat Rev Genet. 2001; 2: 743-755

Rapid generation of inducible mouse mutants.

Nucleic Acids Res. 2003; 31: e12

Intestinal Crypt Homeostasis Results from Neutral Competition between Symmetrically Dividing Lgr5 Stem Cells.

Cell. 2010; 143: 134-144

Genetic lineage tracing with multiple DNA recombinases: A user’s guide for conducting more precise cell fate mapping studies.

Journal of Biological Chemistry. 2020; 295: 6413-6424Senecoff J.F. Rossmeissl P.J. Cox M.M.

DNA recognition by the FLP recombinase of the yeast 2 μ plasmid.

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High-Efficiency FLP and ΦC31 Site-Specific Recombination in Mammalian Cells.

PLoS ONE. 2007; 2: e162

DNA recombination with a heterospecific Cre homolog identified from comparison of the pac-c1 regions of P1-related phages.

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Transgenic mice for intersectional targeting of neural sensors and effectors with high specificity and performance.

Neuron. 2015; 85: 942-958

Redefining the serotonergic system by genetic lineage.

Nat Neurosci. 2008; 11: 417-419

Split-Cre Complementation Indicates Coincident Activity of Different Genes In Vivo.

PLoS ONE. 2009; 4e4286

Intersectional Cre Driver Lines Generated Using Split-Intein Mediated Split-Cre Reconstitution.

Sci Rep. 2012; 2: 497

A suite of new Dre recombinase drivers markedly expands the ability to perform intersectional genetic targeting.

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A beginner’s guide to tissue clearing.

Int J Biochem Cell Biol. 2017; 84: 35-39

Single-cell lineage tracing in the mammary gland reveals stochastic clonal dispersion of stem/progenitor cell progeny.

Nat Commun. 2016; 7: 13053

Intraclonal Plasticity in Mammary Tumors Revealed through Large-Scale Single-Cell Resolution 3D Imaging.

Cancer Cell. 2019; 35 (e6): 618-632

Tissue clearing and its applications in neuroscience.

Nat Rev Neurosci. 2020; 21: 61-79

Next-Generation Lineage Tracing and Fate Mapping to Interrogate Development.

Dev Cell. 2021; 56: 7-21

Single-cell mapping of lineage and identity in direct reprogramming.

Nature. 2018; 564: 219-224

Polylox barcoding reveals haematopoietic stem cell fates realized in vivo.

Nature. 2017; 548: 456-460

Resolving Fates and Single-Cell Transcriptomes of Hematopoietic Stem Cell Clones by PolyloxExpress Barcoding.

Cell Stem Cell. 2020; 27 (e8): 383-395

Whole-organism lineage tracing by combinatorial and cumulative genome editing.

Science. 2016; 353: aaf7907

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain.

Nat Biotechnol. 2018; 36: 442-450

An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells.

Cell. 2020; 181 (e27): 1410-1422

Lineage tracing meets single-cell omics: opportunities and challenges.

Nat Rev Genet. 2020; 21: 410-427

Synthetic recording and in situ readout of lineage information in single cells.

Nature. 2017; 541: 107-111

In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription.

Nat Biotechnol. 2020; 38: 66-75

Somatic mutation in single human neurons tracks developmental and transcriptional history.

Science. 2015; 350: 94-98

Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer.

Genome Res. 2017; 27: 1287-1299

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics.

Cell. 2019; 176 (e22): 1325-1339

Mechanisms of Renal Fibrosis.

Annu Rev Physiol. 2018; 80: 309-326

Detection of renin lineage cell transdifferentiation to podocytes in the kidney glomerulus with dual lineage tracing.

Kidney Int. 2018; 93: 1240-1246

Novel 3D analysis using optical tissue clearing documents the evolution of murine rapidly progressive glomerulonephritis.

Kidney Int. 2019; 96: 505-516

Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation with Single-Cell Transcriptomics.

Cell Stem Cell. 2018; 23 (e8): 869-881Ikeda Y. Sun Z. Ru X. Vandenberghe L.H. Humphreys B.D.

Efficient Gene Transfer to Kidney Mesenchymal Cells Using a Synthetic Adeno-Associated Viral Vector.

J Am Soc Nephrol. 2018; 29: 2287-2297

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