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Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

Author

Listed:
  • Keren Bahar Halpern

    (Weizmann Institute of Science)

  • Rom Shenhav

    (Weizmann Institute of Science)

  • Orit Matcovitch-Natan

    (Weizmann Institute of Science)

  • Beáta Tóth

    (Weizmann Institute of Science)

  • Doron Lemze

    (Weizmann Institute of Science)

  • Matan Golan

    (Weizmann Institute of Science)

  • Efi E. Massasa

    (Weizmann Institute of Science)

  • Shaked Baydatch

    (Weizmann Institute of Science)

  • Shanie Landen

    (Weizmann Institute of Science)

  • Andreas E. Moor

    (Weizmann Institute of Science)

  • Alexander Brandis

    (Biological Services, Weizmann Institute of Science)

  • Amir Giladi

    (Weizmann Institute of Science)

  • Avigail Stokar-Avihail

    (Weizmann Institute of Science)

  • Eyal David

    (Weizmann Institute of Science)

  • Ido Amit

    (Weizmann Institute of Science)

  • Shalev Itzkovitz

    (Weizmann Institute of Science)

Abstract

Single-molecule fluorescence in situ hybridization is performed to identify several landmark genes in the liver and their level of expression in single-cell RNA sequencing is used to spatially reconstruct the zonation of all liver genes.

Suggested Citation

  • Keren Bahar Halpern & Rom Shenhav & Orit Matcovitch-Natan & Beáta Tóth & Doron Lemze & Matan Golan & Efi E. Massasa & Shaked Baydatch & Shanie Landen & Andreas E. Moor & Alexander Brandis & Amir Gilad, 2017. "Single-cell spatial reconstruction reveals global division of labour in the mammalian liver," Nature, Nature, vol. 542(7641), pages 352-356, February.
    • Handle: RePEc:nat:nature:v:542:y:2017:i:7641:d:10.1038_nature21065
    DOI: 10.1038/nature21065
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    Cited by:

    1. Sun Woo Sophie Kang & Rory P. Cunningham & Colin B. Miller & Lauryn A. Brown & Constance M. Cultraro & Adam Harned & Kedar Narayan & Jonathan Hernandez & Lisa M. Jenkins & Alexei Lobanov & Maggie Cam , 2024. "A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Jingyang Qian & Jie Liao & Ziqi Liu & Ying Chi & Yin Fang & Yanrong Zheng & Xin Shao & Bingqi Liu & Yongjin Cui & Wenbo Guo & Yining Hu & Hudong Bao & Penghui Yang & Qian Chen & Mingxiao Li & Bing Zha, 2023. "Reconstruction of the cell pseudo-space from single-cell RNA sequencing data with scSpace," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    3. Zoe Piran & Mor Nitzan, 2024. "SiFT: uncovering hidden biological processes by probabilistic filtering of single-cell data," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    4. Tomaz Martini & Cédric Gobet & Andrea Salati & Jérôme Blanc & Aart Mookhoek & Michael Reinehr & Graham Knott & Jessica Sordet-Dessimoz & Felix Naef, 2024. "A sexually dimorphic hepatic cycle of periportal VLDL generation and subsequent pericentral VLDLR-mediated re-uptake," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    5. Yuan Guan & Annika Enejder & Meiyue Wang & Zhuoqing Fang & Lu Cui & Shih-Yu Chen & Jingxiao Wang & Yalun Tan & Manhong Wu & Xinyu Chen & Patrik K. Johansson & Issra Osman & Koshi Kunimoto & Pierre Rus, 2021. "A human multi-lineage hepatic organoid model for liver fibrosis," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    6. Franziska Hildebrandt & Alma Andersson & Sami Saarenpää & Ludvig Larsson & Noémi Van Hul & Sachie Kanatani & Jan Masek & Ewa Ellis & Antonio Barragan & Annelie Mollbrink & Emma R. Andersson & Joakim L, 2021. "Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    7. Manuel Neumann & Xiaocai Xu & Cezary Smaczniak & Julia Schumacher & Wenhao Yan & Nils Blüthgen & Thomas Greb & Henrik Jönsson & Jan Traas & Kerstin Kaufmann & Jose M. Muino, 2022. "A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    8. Francesca Lazzeri-Barcelo & Nuria Oliva-Vilarnau & Marion Baniol & Barbara Leibiger & Olaf Bergmann & Volker M. Lauschke & Ingo B. Leibiger & Noah Moruzzi & Per-Olof Berggren, 2024. "Intraocular liver spheroids for non-invasive high-resolution in vivo monitoring of liver cell function," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    9. Zhiyuan Yuan & Yisi Li & Minglei Shi & Fan Yang & Juntao Gao & Jianhua Yao & Michael Q. Zhang, 2022. "SOTIP is a versatile method for microenvironment modeling with spatial omics data," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    10. Ana Belén Plata-Gómez & Lucía Prado-Rivas & Alba Sanz & Nerea Deleyto-Seldas & Fernando García & Celia Calle Arregui & Camila Silva & Eduardo Caleiras & Osvaldo Graña-Castro & Elena Piñeiro-Yáñez & Jo, 2024. "Hepatic nutrient and hormone signaling to mTORC1 instructs the postnatal metabolic zonation of the liver," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    11. Jie Fang & Shivendra Singh & Changde Cheng & Sivaraman Natarajan & Heather Sheppard & Ahmed Abu-Zaid & Adam D. Durbin & Ha Won Lee & Qiong Wu & Jacob Steele & Jon P. Connelly & Hongjian Jin & Wenan Ch, 2023. "Genome-wide mapping of cancer dependency genes and genetic modifiers of chemotherapy in high-risk hepatoblastoma," Nature Communications, Nature, vol. 14(1), pages 1-27, December.
    12. Urban Lendahl & Lars Muhl & Christer Betsholtz, 2022. "Identification, discrimination and heterogeneity of fibroblasts," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    13. Inmaculada Ruz-Maldonado & John T. Gonzalez & Hanming Zhang & Jonathan Sun & Alicia Bort & Inamul Kabir & Richard G. Kibbey & Yajaira Suárez & Daniel M. Greif & Carlos Fernández-Hernando, 2024. "Heterogeneity of hepatocyte dynamics restores liver architecture after chemical, physical or viral damage," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
    14. Kristina Handler & Karsten Bach & Costanza Borrelli & Salvatore Piscuoglio & Xenia Ficht & Ilhan E. Acar & Andreas E. Moor, 2023. "Fragment-sequencing unveils local tissue microenvironments at single-cell resolution," Nature Communications, Nature, vol. 14(1), pages 1-17, December.

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