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Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

Author

Listed:
  • Barbara Treutlein

    (Stanford University School of Medicine and Howard Hughes Medical Institute)

  • Doug G. Brownfield

    (Stanford University School of Medicine and Howard Hughes Medical Institute)

  • Angela R. Wu

    (Stanford University School of Medicine and Howard Hughes Medical Institute)

  • Norma F. Neff

    (Stanford University School of Medicine and Howard Hughes Medical Institute)

  • Gary L. Mantalas

    (Stanford University School of Medicine and Howard Hughes Medical Institute)

  • F. Hernan Espinoza

    (Stanford University School of Medicine and Howard Hughes Medical Institute)

  • Tushar J. Desai

    (Stanford University School of Medicine)

  • Mark A. Krasnow

    (Stanford University School of Medicine and Howard Hughes Medical Institute)

  • Stephen R. Quake

    (Stanford University School of Medicine and Howard Hughes Medical Institute)

Abstract

Single-cell transcriptome analysis enables the direct measurement of cell types and lineage hierarchies of the developing distal lung epithelium and identifies a population of bipotential alveolar progenitor cells.

Suggested Citation

  • Barbara Treutlein & Doug G. Brownfield & Angela R. Wu & Norma F. Neff & Gary L. Mantalas & F. Hernan Espinoza & Tushar J. Desai & Mark A. Krasnow & Stephen R. Quake, 2014. "Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq," Nature, Nature, vol. 509(7500), pages 371-375, May.
    • Handle: RePEc:nat:nature:v:509:y:2014:i:7500:d:10.1038_nature13173
    DOI: 10.1038/nature13173
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    Cited by:

    1. Angeles Arzalluz-Luque & Pedro Salguero & Sonia Tarazona & Ana Conesa, 2022. "acorde unravels functionally interpretable networks of isoform co-usage from single cell data," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    2. Ran Wang & Xianfa Yang & Jiehui Chen & Lin Zhang & Jonathan A. Griffiths & Guizhong Cui & Yingying Chen & Yun Qian & Guangdun Peng & Jinsong Li & Liantang Wang & John C. Marioni & Patrick P. L. Tam & , 2023. "Time space and single-cell resolved tissue lineage trajectories and laterality of body plan at gastrulation," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    3. Bobby Ranjan & Wenjie Sun & Jinyu Park & Kunal Mishra & Florian Schmidt & Ronald Xie & Fatemeh Alipour & Vipul Singhal & Ignasius Joanito & Mohammad Amin Honardoost & Jacy Mei Yun Yong & Ee Tzun Koh &, 2021. "DUBStepR is a scalable correlation-based feature selection method for accurately clustering single-cell data," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    4. Cornelia Fuetterer & Thomas Augustin & Christiane Fuchs, 2020. "Adapted single-cell consensus clustering (adaSC3)," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 14(4), pages 885-896, December.
    5. Minzhe Guo & Michael P. Morley & Cheng Jiang & Yixin Wu & Guangyuan Li & Yina Du & Shuyang Zhao & Andrew Wagner & Adnan Cihan Cakar & Michal Kouril & Kang Jin & Nathan Gaddis & Joseph A. Kitzmiller & , 2023. "Guided construction of single cell reference for human and mouse lung," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    6. Kuei-Pin Chung & Chih-Ning Cheng & Yi-Jung Chen & Chia-Lang Hsu & Yen-Lin Huang & Min-Shu Hsieh & Han-Chun Kuo & Ya-Ting Lin & Yi-Hsiu Juan & Kiichi Nakahira & Yen-Fu Chen & Wei-Lun Liu & Sheng-Yuan R, 2024. "Alveolar epithelial cells mitigate neutrophilic inflammation in lung injury through regulating mitochondrial fatty acid oxidation," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
    7. Dalia Hassan & Jichao Chen, 2024. "CEBPA restricts alveolar type 2 cell plasticity during development and injury-repair," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    8. Douglas G. Brownfield & Alex Diaz Arce & Elisa Ghelfi & Astrid Gillich & Tushar J. Desai & Mark A. Krasnow, 2022. "Alveolar cell fate selection and lifelong maintenance of AT2 cells by FGF signaling," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    9. Michael J. Geuenich & Dae-won Gong & Kieran R. Campbell, 2024. "The impacts of active and self-supervised learning on efficient annotation of single-cell expression data," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    10. Francisco X. Galdos & Sidra Xu & William R. Goodyer & Lauren Duan & Yuhsin V. Huang & Soah Lee & Han Zhu & Carissa Lee & Nicholas Wei & Daniel Lee & Sean M. Wu, 2022. "devCellPy is a machine learning-enabled pipeline for automated annotation of complex multilayered single-cell transcriptomic data," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    11. Qi Liu & Charles A Herring & Quanhu Sheng & Jie Ping & Alan J Simmons & Bob Chen & Amrita Banerjee & Wei Li & Guoqiang Gu & Robert J Coffey & Yu Shyr & Ken S Lau, 2018. "Quantitative assessment of cell population diversity in single-cell landscapes," PLOS Biology, Public Library of Science, vol. 16(10), pages 1-29, October.
    12. Kieran R Campbell & Christopher Yau, 2016. "Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference," PLOS Computational Biology, Public Library of Science, vol. 12(11), pages 1-20, November.
    13. Seunghan Han & Bomin Kim & Do Young Hyeon & Daeun Jeong & Jaechan Ryu & Jae-Sung Nam & Yoon Ha Choi & Bo-Ram Kim & Sang Chul Park & Youn Wook Chung & Sung Jae Shin & June-Yong Lee & Jong Kyoung Kim & , 2024. "Distinctive CD39+CD9+ lung interstitial macrophages suppress IL-23/Th17-mediated neutrophilic asthma by inhibiting NETosis," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    14. Md Tauhidul Islam & Jen-Yeu Wang & Hongyi Ren & Xiaomeng Li & Masoud Badiei Khuzani & Shengtian Sang & Lequan Yu & Liyue Shen & Wei Zhao & Lei Xing, 2022. "Leveraging data-driven self-consistency for high-fidelity gene expression recovery," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    15. Jingyu Zhang & Hengyu Chen & Ruoyan Li & David A Taft & Guang Yao & Fan Bai & Jianhua Xing, 2019. "Spatial clustering and common regulatory elements correlate with coordinated gene expression," PLOS Computational Biology, Public Library of Science, vol. 15(3), pages 1-16, March.
    16. Christopher W. Murray & Jennifer J. Brady & Mingqi Han & Hongchen Cai & Min K. Tsai & Sarah E. Pierce & Ran Cheng & Janos Demeter & David M. Feldser & Peter K. Jackson & David B. Shackelford & Monte M, 2022. "LKB1 drives stasis and C/EBP-mediated reprogramming to an alveolar type II fate in lung cancer," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    17. Zhoufeng Wang & Zhe Li & Kun Zhou & Chengdi Wang & Lili Jiang & Li Zhang & Ying Yang & Wenxin Luo & Wenliang Qiao & Gang Wang & Yinyun Ni & Shuiping Dai & Tingting Guo & Guiyi Ji & Minjie Xu & Yiying , 2021. "Deciphering cell lineage specification of human lung adenocarcinoma with single-cell RNA sequencing," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    18. Nevin Witman & Chikai Zhou & Timm Häneke & Yao Xiao & Xiaoting Huang & Eduarde Rohner & Jesper Sohlmér & Niels Grote Beverborg & Miia L. Lehtinen & Kenneth R. Chien & Makoto Sahara, 2023. "Placental growth factor exerts a dual function for cardiomyogenesis and vasculogenesis during heart development," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    19. Chieh Lin & Jun Ding & Ziv Bar-Joseph, 2020. "Inferring TF activation order in time series scRNA-Seq studies," PLOS Computational Biology, Public Library of Science, vol. 16(2), pages 1-19, February.
    20. Ruihua Zhang & Qun Liu & Shanshan Pan & Yingying Zhang & Yating Qin & Xiao Du & Zengbao Yuan & Yongrui Lu & Yue Song & Mengqi Zhang & Nannan Zhang & Jie Ma & Zhe Zhang & Xiaodong Jia & Kun Wang & Shun, 2023. "A single-cell atlas of West African lungfish respiratory system reveals evolutionary adaptations to terrestrialization," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    21. Ming-Wen Hu & Dong Won Kim & Sheng Liu & Donald J Zack & Seth Blackshaw & Jiang Qian, 2019. "PanoView: An iterative clustering method for single-cell RNA sequencing data," PLOS Computational Biology, Public Library of Science, vol. 15(8), pages 1-17, August.

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