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 journalArticlepeer-review

2 Scopus citations


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 languageAmerican English
Article number100794
JournalSTAR Protocols
Issue number4
StatePublished - 17 Dec 2021

Bibliographical note

Publisher Copyright:
© 2021 The Authors


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


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