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

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

doi:10.1016/j.xpro.2021.100794

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

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

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Abstract

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).

Original language	English
Article number	100794
Journal	STAR Protocols
Volume	2
Issue number	4
DOIs	https://doi.org/10.1016/j.xpro.2021.100794
State	Published - 17 Dec 2021

Bibliographical note

Publisher Copyright:
© 2021 The Authors

Keywords

Cell Biology
Cell culture
High Throughput Screening
Molecular Biology
RNAseq
Sequence analysis
Sequencing
Single Cell

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10.1016/j.xpro.2021.100794

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abstract = "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).",

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AU - Ram, Oren

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

Abstract

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Keywords

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