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Journal articles on the topic 'Cell lineage tracing'

Author: Grafiati

Published: 5 June 2025

Last updated: 2 August 2025

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1

Stern, Claudio D., and Scott E. Fraser. "Tracing the lineage of tracing cell lineages." Nature Cell Biology 3, no. 9 (2001): E216—E218. http://dx.doi.org/10.1038/ncb0901-e216.

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2

Burgess, Darren J. "Tracing cell-lineage histories." Nature Reviews Genetics 19, no. 6 (2018): 327. http://dx.doi.org/10.1038/s41576-018-0015-0.

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3

Abyzov, Alexej, and Flora M. Vaccarino. "Cell Lineage Tracing and Cellular Diversity in Humans." Annual Review of Genomics and Human Genetics 21, no. 1 (2020): 101–16. http://dx.doi.org/10.1146/annurev-genom-083118-015241.

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Tracing cell lineages is fundamental for understanding the rules governing development in multicellular organisms and delineating complex biological processes involving the differentiation of multiple cell types with distinct lineage hierarchies. In humans, experimental lineage tracing is unethical, and one has to rely on natural-mutation markers that are created within cells as they proliferate and age. Recent studies have demonstrated that it is now possible to trace lineages in normal, noncancerous cells with a variety of data types using natural variations in the nuclear and mitochondrial

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4

Jarchum, Irene. "Tracing cell lineage with 5hmC." Nature Methods 13, no. 9 (2016): 710–11. http://dx.doi.org/10.1038/nmeth.3986.

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5

Wang, Lin, Zheng Yin, Wenjuan Dong, et al. "Abstract 2487: LINMAP: A framework for comprehensive cell division lineage reconstruction via molecular barcoding and machine learning." Cancer Research 85, no. 8_Supplement_1 (2025): 2487. https://doi.org/10.1158/1538-7445.am2025-2487.

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Abstract Purpose: Reconstructing cell division lineages across generations is central to understanding developmental biology, cancer progression, cell differentiation, drug resistance, and tissue aging. By integrating CRISPR-Cas9 induced gene editing with single cell RNA-Seq, high-resolution lineage tracing through molecular barcoding becomes feasible. However, tracking mutation evolution across successive guide RNA edits, especially with homing guide RNA (hgRNA) technology, poses challenges due to ongoing dynamic retargeting and genetic modifications that complicate lineage reconstruction. Me

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Liu, Kuo, Hengwei Jin, and Bin Zhou. "Genetic lineage tracing with multiple DNA recombinases: A user's guide for conducting more precise cell fate mapping studies." Journal of Biological Chemistry 295, no. 19 (2020): 6413–24. http://dx.doi.org/10.1074/jbc.rev120.011631.

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Site-specific recombinases, such as Cre, are a widely used tool for genetic lineage tracing in the fields of developmental biology, neural science, stem cell biology, and regenerative medicine. However, nonspecific cell labeling by some genetic Cre tools remains a technical limitation of this recombination system, which has resulted in data misinterpretation and led to many controversies in the scientific community. In the past decade, to enhance the specificity and precision of genetic targeting, researchers have used two or more orthogonal recombinases simultaneously for labeling cell lineag

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7

Yunusova, A. M., and N. R. Battulin. "Cell-marking techniques for cell lineage tracing." Vavilov Journal of Genetics and Breeding 20, no. 6 (2016): 909–17. http://dx.doi.org/10.18699/vj16.211.

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8

Buckingham, Margaret E., and Sigolène M. Meilhac. "Tracing Cells for Tracking Cell Lineage and Clonal Behavior." Developmental Cell 21, no. 3 (2011): 394–409. http://dx.doi.org/10.1016/j.devcel.2011.07.019.

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9

Kreslavsky, Taras, Annette I. Garbe, Andreas Krueger та Harald von Boehmer. "T cell receptor–instructed αβ versus γδ lineage commitment revealed by single-cell analysis". Journal of Experimental Medicine 205, № 5 (2008): 1173–86. http://dx.doi.org/10.1084/jem.20072425.

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αβ and γδ T cell lineages develop in the thymus from a common precursor. It is unclear at which stage of development commitment to these lineages takes place and in which way T cell receptor signaling contributes to the process. Recently, it was demonstrated that strong TCR signals favor γδ lineage development, whereas weaker TCR signals promote αβ lineage fate. Two models have been proposed to explain these results. The first model suggests that commitment occurs after TCR expression and TCR signaling directly instructs lymphocytes to adopt one or the other lineage fate. The second model sugg

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10

Burgess, Darren J. "Genome editing for cell lineage tracing." Nature Reviews Genetics 17, no. 8 (2016): 435. http://dx.doi.org/10.1038/nrg.2016.80.

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11

Kester, Lennart, and Alexander van Oudenaarden. "Single-Cell Transcriptomics Meets Lineage Tracing." Cell Stem Cell 23, no. 2 (2018): 166–79. http://dx.doi.org/10.1016/j.stem.2018.04.014.

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12

Jang, Jinho, Kyung-Pil Ko, Jie Zhang, and Jae-Il Park. "Abstract 7490: Uncovering rare cellular populations in esophageal preneoplasia through genetic perturbation tracking and scRNA-seq." Cancer Research 85, no. 8_Supplement_1 (2025): 7490. https://doi.org/10.1158/1538-7445.am2025-7490.

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Abstract The early detection and characterization of rare cellular populations in preneoplastic lesions are crucial for understanding cancer initiation and progression, as well as for identifying novel therapeutic targets. Rare cell populations, often overlooked due to their low abundance, play pivotal roles in shaping the tumor microenvironment and driving disease development. In this study, we employed a lineage tracing system based on tracing vectors introduced into a 2D cell line model of esophageal preneoplasia. This approach allowed us to track genetic perturbations that accumulate durin

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13

Yao, Mingze, Tinglin Ren, Yuanqing Pan, et al. "A New Generation of Lineage Tracing Dynamically Records Cell Fate Choices." International Journal of Molecular Sciences 23, no. 9 (2022): 5021. http://dx.doi.org/10.3390/ijms23095021.

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Reconstructing the development of lineage relationships and cell fate mapping has been a fundamental problem in biology. Using advanced molecular biology and single-cell RNA sequencing, we have profiled transcriptomes at the single-cell level and mapped cell fates during development. Recently, CRISPR/Cas9 barcode editing for large-scale lineage tracing has been used to reconstruct the pseudotime trajectory of cells and improve lineage tracing accuracy. This review presents the progress of the latest CbLT (CRISPR-based Lineage Tracing) and discusses the current limitations and potential technic

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14

Innes, James, Sebastian Brandner, and Silvia Marino. "Multi-colour lineage tracing to asses intra-tumour heterogeneity in glioblastoma multiforme." Neuro-Oncology 21, Supplement_4 (2019): iv1. http://dx.doi.org/10.1093/neuonc/noz167.001.

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Abstract Background Glioblastoma multiforme (GBM) represents nearly 50% of all malignant brain tumours. Molecular and genomic diagnostics are beginning to unravel the variation between individual tumours. However, there is growing evidence that cellular heterogeneity exists within a single malignancy. Singe cell analysis has demonstrated the presence of subpopulations corresponding to distinct expression profiles. Objective and experimental approach characterisation of the intratumor heterogeneity is essential to understand biological behaviour and therapy response. Through combining a genetic

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15

Zhang, MingJun, Kathy O. Lui, and Bin Zhou. "Application of New Lineage Tracing Techniques in Cardiovascular Development and Physiology." Circulation Research 134, no. 4 (2024): 445–58. http://dx.doi.org/10.1161/circresaha.123.323179.

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Cardiovascular disease has been the leading cause of mortality and morbidity worldwide in the past 3 decades. Multiple cell lineages undergo dynamic alternations in gene expression, cell state determination, and cell fate conversion to contribute, adapt, and even modulate the pathophysiological processes during disease progression. There is an urgent need to understand the intricate cellular and molecular underpinnings of cardiovascular cell development in homeostasis and pathogenesis. Recent strides in lineage tracing methodologies have revolutionized our understanding of cardiovascular biolo

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16

Upadhaya, Samik, Catherine M. Sawai, Efthymia Papalexi, et al. "Kinetics of adult hematopoietic stem cell differentiation in vivo." Journal of Experimental Medicine 215, no. 11 (2018): 2815–32. http://dx.doi.org/10.1084/jem.20180136.

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Adult hematopoiesis has been studied in terms of progenitor differentiation potentials, whereas its kinetics in vivo is poorly understood. We combined inducible lineage tracing of endogenous adult hematopoietic stem cells (HSCs) with flow cytometry and single-cell RNA sequencing to characterize early steps of hematopoietic differentiation in the steady-state. Labeled cells, comprising primarily long-term HSCs and some short-term HSCs, produced megakaryocytic lineage progeny within 1 wk in a process that required only two to three cell divisions. Erythroid and myeloid progeny emerged simultaneo

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17

Blanpain, Cédric, and Benjamin D. Simons. "Unravelling stem cell dynamics by lineage tracing." Nature Reviews Molecular Cell Biology 14, no. 8 (2013): 489–502. http://dx.doi.org/10.1038/nrm3625.

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18

Zahn, Laura M. "Tracing development of the dendritic cell lineage." Science 356, no. 6342 (2017): 1040.11–1042. http://dx.doi.org/10.1126/science.356.6342.1040-k.

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19

Tang, Lin. "Integrating lineage tracing and single-cell analysis." Nature Methods 17, no. 4 (2020): 359. http://dx.doi.org/10.1038/s41592-020-0802-3.

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20

Bao, Z., J. I. Murray, T. Boyle, S. L. Ooi, M. J. Sandel, and R. H. Waterston. "Automated cell lineage tracing in Caenorhabditis elegans." Proceedings of the National Academy of Sciences 103, no. 8 (2006): 2707–12. http://dx.doi.org/10.1073/pnas.0511111103.

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21

Gargioli, C. "Cell lineage tracing during Xenopus tail regeneration." Development 131, no. 11 (2004): 2669–79. http://dx.doi.org/10.1242/dev.01155.

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22

Gimlich, Robert L., and Jochen Braun. "Improved fluorescent compounds for tracing cell lineage." Developmental Biology 109, no. 2 (1985): 509–14. http://dx.doi.org/10.1016/0012-1606(85)90476-2.

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23

Lee, Eunmi, and Yibin Kang. "Lineage tracing reveals metastatic dynamics." Cancer Cell 39, no. 8 (2021): 1050–52. http://dx.doi.org/10.1016/j.ccell.2021.06.005.

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24

Chari, Sheila, Anh Nguyen, Jonathan Saxe, and Deborah J. Sweet. "Lineage Tracing across 10 Years." Cell Stem Cell 20, no. 6 (2017): 733–34. http://dx.doi.org/10.1016/j.stem.2017.05.017.

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25

Yu, Xuexin, Jing Hu, Yuhao Tan, Mingyao Pan, Hongyi Zhang, and Bo Li. "MitoTracer facilitates the identification of informative mitochondrial mutations for precise lineage reconstruction." PLOS Computational Biology 21, no. 6 (2025): e1013090. https://doi.org/10.1371/journal.pcbi.1013090.

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Mitochondrial (MT) mutations serve as natural genetic markers for inferring clonal relationships using single cell sequencing data. However, the fundamental challenge of MT mutation-based lineage tracing is automated identification of informative MT mutations. Here, we introduced an open-source computational algorithm called “MitoTracer”, which accurately identified clonally informative MT mutations and inferred evolutionary lineage from scRNA-seq or scATAC-seq samples. We benchmarked MitoTracer using the ground-truth experimental lineage sequencing data and demonstrated its superior performan

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26

Vogt, Nina. "Lineage tracing with Polylox barcodes." Nature Methods 14, no. 10 (2017): 940. http://dx.doi.org/10.1038/nmeth.4451.

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27

Tang, Lei. "Greater diversity for lineage tracing." Nature Methods 20, no. 12 (2023): 1872. http://dx.doi.org/10.1038/s41592-023-02131-3.

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28

Tang, Weiyi, and Marianne E. Bronner. "Neural crest lineage analysis: from past to future trajectory." Development 147, no. 20 (2020): dev193193. http://dx.doi.org/10.1242/dev.193193.

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ABSTRACTSince its discovery 150 years ago, the neural crest has intrigued investigators owing to its remarkable developmental potential and extensive migratory ability. Cell lineage analysis has been an essential tool for exploring neural crest cell fate and migration routes. By marking progenitor cells, one can observe their subsequent locations and the cell types into which they differentiate. Here, we review major discoveries in neural crest lineage tracing from a historical perspective. We discuss how advancing technologies have refined lineage-tracing studies, and how clonal analysis can

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29

Unterweger, Iris A., Julie Klepstad, Edouard Hannezo, Pia R. Lundegaard, Ala Trusina, and Elke A. Ober. "Lineage tracing identifies heterogeneous hepatoblast contribution to cell lineages and postembryonic organ growth dynamics." PLOS Biology 21, no. 10 (2023): e3002315. http://dx.doi.org/10.1371/journal.pbio.3002315.

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To meet the physiological demands of the body, organs need to establish a functional tissue architecture and adequate size as the embryo develops to adulthood. In the liver, uni- and bipotent progenitor differentiation into hepatocytes and biliary epithelial cells (BECs), and their relative proportions, comprise the functional architecture. Yet, the contribution of individual liver progenitors at the organ level to both fates, and their specific proportion, is unresolved. Combining mathematical modelling with organ-wide, multispectral FRaeppli-NLS lineage tracing in zebrafish, we demonstrate t

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30

Zhitomirsky, Benny, Jideofor Ezike, Elizabeth Hopkins, et al. "Abstract 2859: High-resolution lineage tracing for the study of cancer drug persistence at the single-cell level." Cancer Research 83, no. 7_Supplement (2023): 2859. http://dx.doi.org/10.1158/1538-7445.am2023-2859.

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Abstract Cancer drug persistence allows small fractions of otherwise drug-sensitive populations of cancer cells to survive treatment with anti-cancer drugs. Unlike drug resistance, persistence mechanisms are not driven by genetic mutations, and are thus considered reversible after a ‘drug holiday’ period. While most persistent cells remain in cell cycle arrest under drug treatment, recent work with EGFR-mutant Non-Small Cell Lung Cancer (NSCLC) cell lines has demonstrated that a small fraction of persister cells continue to undergo cell divisions under treatment with EGFR inhibitors. Thus, per

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31

Gardner, Andrea L., Lan Zheng, Daylin Morgan, Kennedy Howland, and Amy Brock. "Abstract B037: ClonMapper Duo: An scRNAseq compatible lineage tracing method to track cell-cell fusion at single-cell resolution." Cancer Research 84, no. 3_Supplement_2 (2024): B037. http://dx.doi.org/10.1158/1538-7445.canevol23-b037.

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Abstract Spontaneous cell-cell fusion in cancer can generate genetic heterogeneity and often leads to more pathological phenotypes. While the consequences of cell-cell fusion in cancer continue to be revealed, few tools exist to determine the mechanisms and cell states which promote cell-cell fusion. To meet this need, we engineered ClonMapper Duo, a two-color, two-index expressed barcoding system which allows tracking of cell-cell fusion using live-cell imaging and lineage tracing of fusion cells in scRNAseq. The ClonMapper Duo system was created by modifying the ClonMapper DNA barcoding syst

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32

McKenna, Aaron, and James A. Gagnon. "Recording development with single cell dynamic lineage tracing." Development 146, no. 12 (2019): dev169730. http://dx.doi.org/10.1242/dev.169730.

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33

Kalhor, Kian, and George M. Church. "Single-Cell CRISPR-Based Lineage Tracing in Mice." Biochemistry 58, no. 48 (2019): 4775–76. http://dx.doi.org/10.1021/acs.biochem.9b00688.

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34

Wang, Bingyan, Alvin Muliono, Roberto Alvarez, and Mark Sussman. "Cardiac Progenitor Cell Lineage Tracing During Embryonic Cardiomyogenesis." Journal of Molecular and Cellular Cardiology 112 (November 2017): 138. http://dx.doi.org/10.1016/j.yjmcc.2017.07.027.

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35

Ajisebutu, A., F. Fan, C. Gui, et al. "F.2 Single cell CRISPR/Cas-9 lineage tracing reveals fitness axis in glioblastoma." Canadian Journal of Neurological Sciences / Journal Canadien des Sciences Neurologiques 52, s1 (2025): S14. https://doi.org/10.1017/cjn.2025.10180.

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Background: We’ve adopted a novel approach that combines cellular barcoding with CRISPR/Cas-9 technology and single-cell RNA sequencing known as continuous lineage tracing to track the development, treatment and inevitable recurrence of glioblastoma. Methods: Patient derived glioma initiating cell lines were engineered with expressed DNA barcodes with CRISPR/Cas-9 targets and engrafted into NOD scid-mice. Clonal and relationships are surmised through identification of expressed barcodes, and cells were characterized by their transcriptional profiles. Phylogenetic lineage trees are created usin

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Liu, Kuo, Muxue Tang, Hengwei Jin, et al. "Triple-cell lineage tracing by a dual reporter on a single allele." Journal of Biological Chemistry 295, no. 3 (2019): 690–700. http://dx.doi.org/10.1074/jbc.ra119.011349.

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Genetic lineage tracing is widely used to study organ development and tissue regeneration. Multicolor reporters are a powerful platform for simultaneously tracking discrete cell populations. Here, combining Dre-rox and Cre-loxP systems, we generated a new dual-recombinase reporter system, called Rosa26 traffic light reporter (R26-TLR), to monitor red, green, and yellow fluorescence. Using this new reporter system with the three distinct fluorescent reporters combined on one allele, we found that the readouts of the two recombinases Cre and Dre simultaneously reflect Cre+Dre−, Cre−Dre+, and Cre

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37

Lavaert, M., N. Vandamme, Y. Saeys, and T. Taghon. "PF460 SINGLE CELL RNASEQ REVEALS THE IN VIVO DIFFERENTIATION POTENTIAL AND TRANSCRIPTIONAL DYNAMICS OF IMMATURE HUMAN THYMOCYTES." HemaSphere 3, S1 (2019): 181. http://dx.doi.org/10.1002/j.2572-9241.2019.tb00059.x.

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Background:T cell development depends on the colonization of the thymus by multipotent progenitor cells from the bone marrow. There, these precursor cells are gradually reprogrammed into committed T cell progenitors that have lost the developmental potential towards other hematopoietic lineages. While lineage tracing experiments in mice have provided evidence to which non T‐cell lineages these early T cell precursors differentiate in vivo, it remains unclear in human which blood cell lineages can originate from early T cell precursors. In vitro differentiation experiments have revealed erythro

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Sepulveda-Rincon, L. P., D. Dube, P. Adenot, et al. "78 NONINVASIVE CELL LINEAGE TRACING IN BOVINE EMBRYOS FROM 2-CELL STAGE UP TO BLASTOCYST STAGE." Reproduction, Fertility and Development 27, no. 1 (2015): 132. http://dx.doi.org/10.1071/rdv27n1ab78.

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The first lineage specification occurs during pre-implantation mammalian development. At the blastocyst stage, 2 cell lineages can be distinguished: the inner cell mass (ICM) and the trophectoderm (TE). The exact timing when embryo cells are skewed to these lineages is not clearly determined in mammalian species. In murine embryos, it has been suggested that the first cleavage plane might be related to the embryonic-abembryonic (Em-Ab) axis at blastocyst stage. Thus, the daughter cells of the 2-cell embryo might already be predisposed to a specific cell lineage further on development. The obje

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39

Annusver, Karl, David Fernandez, Diana Pereira, Jean-François Nicolas, Maria Kasper, and Inês Sequeira. "O01 Mapping the cellular and molecular dynamics of mouse and human hair follicles reveals mechanisms of hair growth." British Journal of Dermatology 190, no. 6 (2024): e68-e68. http://dx.doi.org/10.1093/bjd/ljae105.001.

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Abstract Introduction and aims Tissue homeostasis in continuously renewing organs, such as the skin, rely on orchestrated cellular and molecular dynamics. The hair follicle (HF) is characterized by distinct keratinocytes organized in transcriptionally and functionally distinct concentric HF layers. The anagen progenitor cells (also called germinative layer cells) are located juxtaposed to the dermal papilla and give rise to each of the differentiated layers. Despite this well-known high level of organization and cell-lineage separation, it is still unclear how the germinative layer cells coord

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Fink, Juergen, Amanda Andersson-Rolf, and Bon-Kyoung Koo. "Adult stem cell lineage tracing and deep tissue imaging." BMB Reports 48, no. 12 (2015): 655–67. http://dx.doi.org/10.5483/bmbrep.2015.48.12.249.

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41

Rodriguez-Fraticelli, Alejo E., and Fernando Camargo. "Systems analysis of hematopoiesis using single-cell lineage tracing." Current Opinion in Hematology 28, no. 1 (2021): 18–27. http://dx.doi.org/10.1097/moh.0000000000000624.

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42

Masuyama, Nanami, Hideto Mori, and Nozomu Yachie. "DNA barcodes evolve for high-resolution cell lineage tracing." Current Opinion in Chemical Biology 52 (October 2019): 63–71. http://dx.doi.org/10.1016/j.cbpa.2019.05.014.

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43

Wagner, Daniel E., and Allon M. Klein. "Lineage tracing meets single-cell omics: opportunities and challenges." Nature Reviews Genetics 21, no. 7 (2020): 410–27. http://dx.doi.org/10.1038/s41576-020-0223-2.

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44

Kim, Ik Soo. "DNA Barcoding Technology for Lineage Recording and Tracing to Resolve Cell Fate Determination." Cells 13, no. 1 (2023): 27. http://dx.doi.org/10.3390/cells13010027.

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In various biological contexts, cells receive signals and stimuli that prompt them to change their current state, leading to transitions into a future state. This change underlies the processes of development, tissue maintenance, immune response, and the pathogenesis of various diseases. Following the path of cells from their initial identity to their current state reveals how cells adapt to their surroundings and undergo transformations to attain adjusted cellular states. DNA-based molecular barcoding technology enables the documentation of a phylogenetic tree and the deterministic events of

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45

Pucella, Joseph N., Samik Upadhaya, and Boris Reizis. "The Source and Dynamics of Adult Hematopoiesis: Insights from Lineage Tracing." Annual Review of Cell and Developmental Biology 36, no. 1 (2020): 529–50. http://dx.doi.org/10.1146/annurev-cellbio-020520-114601.

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The generation of all blood cell lineages (hematopoiesis) is sustained throughout the entire life span of adult mammals. Studies using cell transplantation identified the self-renewing, multipotent hematopoietic stem cells (HSCs) as the source of hematopoiesis in adoptive hosts and delineated a hierarchy of HSC-derived progenitors that ultimately yield mature blood cells. However, much less is known about adult hematopoiesis as it occurs in native hosts, i.e., without transplantation. Here we review recent advances in our understanding of native hematopoiesis, focusing in particular on the app

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Sayols, Sergi, Jakub Klassek, Clara Werner, et al. "Signalling codes for the maintenance and lineage commitment of embryonic gastric epithelial progenitors." Development 147, no. 18 (2020): dev188839. http://dx.doi.org/10.1242/dev.188839.

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ABSTRACTThe identity of embryonic gastric epithelial progenitors is unknown. We used single-cell RNA-sequencing, genetic lineage tracing and organoid assays to assess whether Axin2- and Lgr5-expressing cells are gastric progenitors in the developing mouse stomach. We show that Axin2+ cells represent a transient population of embryonic epithelial cells in the forestomach. Lgr5+ cells generate both glandular corpus and squamous forestomach organoids ex vivo. Only Lgr5+ progenitors give rise to zymogenic cells in culture. Modulating the activity of the WNT, BMP and Notch pathways in vivo and ex v

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47

Peterson, Joshua C., Tim P. Kelder, Marie José T. H. Goumans, Monique R. M. Jongbloed, and Marco C. DeRuiter. "The Role of Cell Tracing and Fate Mapping Experiments in Cardiac Outflow Tract Development, New Opportunities through Emerging Technologies." Journal of Cardiovascular Development and Disease 8, no. 5 (2021): 47. http://dx.doi.org/10.3390/jcdd8050047.

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Whilst knowledge regarding the pathophysiology of congenital heart disease (CHDs) has advanced greatly in recent years, the underlying developmental processes affecting the cardiac outflow tract (OFT) such as bicuspid aortic valve, tetralogy of Fallot and transposition of the great arteries remain poorly understood. Common among CHDs affecting the OFT, is a large variation in disease phenotypes. Even though the different cell lineages contributing to OFT development have been studied for many decades, it remains challenging to relate cell lineage dynamics to the morphologic variation observed

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48

Frank, David B., Ian J. Penkala, Jarod A. Zepp, et al. "Early lineage specification defines alveolar epithelial ontogeny in the murine lung." Proceedings of the National Academy of Sciences 116, no. 10 (2019): 4362–71. http://dx.doi.org/10.1073/pnas.1813952116.

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During the stepwise specification and differentiation of tissue-specific multipotent progenitors, lineage-specific transcriptional networks are activated or repressed to orchestrate cell specification. The gas-exchange niche in the lung contains two major epithelial cell types, alveolar type 1 (AT1) and AT2 cells, and the timing of lineage specification of these cells is critical for the correct formation of this niche and postnatal survival. Integrating cell-specific lineage tracing studies, spatially specific mRNA transcript and protein expression, and single-cell RNA-sequencing analysis, we

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49

Padrón-Barthe, Laura, Susana Temiño, Cristina Villa del Campo, Laura Carramolino, Joan Isern, and Miguel Torres. "Clonal analysis identifies hemogenic endothelium as the source of the blood-endothelial common lineage in the mouse embryo." Blood 124, no. 16 (2014): 2523–32. http://dx.doi.org/10.1182/blood-2013-12-545939.

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Key Points Single cell lineage tracing shows early separation of blood-endothelial precursors in the mouse embryo. Hemogenic endothelium in the YS generates the blood-endothelial common lineage and produces definitive precursors.

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50

Forrow, Aden, and Geoffrey Schiebinger. "LineageOT is a unified framework for lineage tracing and trajectory inference." Nature Communications 12, no. 1 (2021). http://dx.doi.org/10.1038/s41467-021-25133-1.

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AbstractUnderstanding the genetic and epigenetic programs that control differentiation during development is a fundamental challenge, with broad impacts across biology and medicine. Measurement technologies like single-cell RNA-sequencing and CRISPR-based lineage tracing have opened new windows on these processes, through computational trajectory inference and lineage reconstruction. While these two mathematical problems are deeply related, methods for trajectory inference are not typically designed to leverage information from lineage tracing and vice versa. Here, we present LineageOT, a unif

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