CloneSeq - Single-cell clonal 3D culture and analysis protocol

Xue Sun; Danny Bavli; Chen Kozulin; Alex Motzik; Amnon Buxboim; Oren Ram

STAR Protocols (Dec 2021)

CloneSeq - Single-cell clonal 3D culture and analysis protocol

Xue Sun,
Danny Bavli,
Chen Kozulin,
Alex Motzik,
Amnon Buxboim,
Oren Ram

Affiliations

Xue Sun: Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel; Corresponding author
Danny Bavli: Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel; Alexander Grass Center for Bioengineering, Benin School of Computer Science and Engineering, Hebrew University of Jerusalem, Jerusalem, Israel; Corresponding author
Chen Kozulin: Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
Alex Motzik: Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
Amnon Buxboim: Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel; Alexander Grass Center for Bioengineering, Benin School of Computer Science and Engineering, Hebrew University of Jerusalem, Jerusalem, Israel; Department of Cell and Developmental Biology, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
Oren Ram: Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel; Corresponding author

Journal volume & issue: Vol. 2, no. 4
p. 100794

Abstract

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Summary: This CloneSeq protocol combines clonal expansion inside 3D hydrogel spheres and droplet-based RNA sequencing to resolve the limited sensitivity of single-cell approaches. CloneSeq can reveal rare subpopulations and support cellular stemness. CloneSeq can be adapted to different biological systems to discover rare subpopulations by leveraging clonal enhanced sensitivity. Important considerations include the hydrogel composition, adaptation of 3D cultured clones to the inDrops system, and inherent adhesive properties of the cells. CloneSeq is only validated for cell lines so far.For complete details on the use and execution of this protocol, please refer to (Bavli et al., 2021).

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

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