Protocol for profiling in vitro intratumor heterogeneity using spatially annotated single-cell sequencing

Myrthe M. Smit; Kate J. Feller; Li You; Miao Ping Chien

doi:10.1016/j.xpro.2023.102447

Protocol for profiling in vitro intratumor heterogeneity using spatially annotated single-cell sequencing

Myrthe M. Smit, Kate J. Feller, Li You, Miao Ping Chien^*

^*Corresponding author for this work

Molecular Genetics

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

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Abstract

Here, we present a protocol for spatially annotated single-cell sequencing, a technique for spatially profiling intratumor heterogeneity with deep single-cell RNA sequencing and single-cell resolution. By combining live-cell imaging and photopatterned illumination, we describe steps to identify regions of interest in an in vitro tumor model, label the selected cells with photoactivatable dyes, and isolate and subject them to scRNAseq. This protocol can be applied to a range of cell lines and could be expanded to tissue sections. For complete details on the use and execution of this protocol, please refer to Smit et al. (2022).¹

Original language	English
Article number	102447
Journal	STAR Protocols
Volume	4
Issue number	3
DOIs	https://doi.org/10.1016/j.xpro.2023.102447
Publication status	Published - 15 Sept 2023

Bibliographical note

Funding Information:
M.-P.C. acknowledges support from the Oncode Institute , the Netherlands; Cancer GenomiCs.nl (CGC), the Netherlands; NWO (Netherlands Organization for Scientific Research) Veni and Vidi Grants, the Netherlands; and Stichting Ammodo and Erasmus MC grant, the Netherlands. M.-P.C. appreciates Josephine Nefkens Stichting’s support on the UFO microscope. We thank Reuven Agami for the kind gift of the MCF10A-H2B-GFP cell line.

Publisher Copyright: © 2023 The Authors

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Protocol for profiling in vitro intratumor heterogeneity using spatially annotated single-cell sequencingFinal published version, 4.5 MBLicence: CC BY

Cite this

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title = "Protocol for profiling in vitro intratumor heterogeneity using spatially annotated single-cell sequencing",

abstract = "Here, we present a protocol for spatially annotated single-cell sequencing, a technique for spatially profiling intratumor heterogeneity with deep single-cell RNA sequencing and single-cell resolution. By combining live-cell imaging and photopatterned illumination, we describe steps to identify regions of interest in an in vitro tumor model, label the selected cells with photoactivatable dyes, and isolate and subject them to scRNAseq. This protocol can be applied to a range of cell lines and could be expanded to tissue sections. For complete details on the use and execution of this protocol, please refer to Smit et al. (2022).1",

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AU - You, Li

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N1 - Funding Information: M.-P.C. acknowledges support from the Oncode Institute , the Netherlands; Cancer GenomiCs.nl (CGC), the Netherlands; NWO (Netherlands Organization for Scientific Research) Veni and Vidi Grants, the Netherlands; and Stichting Ammodo and Erasmus MC grant, the Netherlands. M.-P.C. appreciates Josephine Nefkens Stichting’s support on the UFO microscope. We thank Reuven Agami for the kind gift of the MCF10A-H2B-GFP cell line. Publisher Copyright: © 2023 The Authors

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AB - Here, we present a protocol for spatially annotated single-cell sequencing, a technique for spatially profiling intratumor heterogeneity with deep single-cell RNA sequencing and single-cell resolution. By combining live-cell imaging and photopatterned illumination, we describe steps to identify regions of interest in an in vitro tumor model, label the selected cells with photoactivatable dyes, and isolate and subject them to scRNAseq. This protocol can be applied to a range of cell lines and could be expanded to tissue sections. For complete details on the use and execution of this protocol, please refer to Smit et al. (2022).1

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Protocol for profiling in vitro intratumor heterogeneity using spatially annotated single-cell sequencing

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