Protocol for using single-cell sequencing to study the heterogeneity of NF1 nerve sheath tumors from clinical biospecimens

Xiyuan Zhang; Vishaka Gopalan; Neeraja Syed; Sridhar Hannenhalli; Jack F Shern

doi:10.1016/j.xpro.2023.102297

Protocol for using single-cell sequencing to study the heterogeneity of NF1 nerve sheath tumors from clinical biospecimens

STAR Protoc. 2023 May 10;4(2):102297. doi: 10.1016/j.xpro.2023.102297. Online ahead of print.

Authors

Xiyuan Zhang¹, Vishaka Gopalan², Neeraja Syed³, Sridhar Hannenhalli², Jack F Shern⁴

Affiliations

¹ Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: [email protected].
² Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
³ Pediatric Oncology Branch Childhood Cancer Data Initiative, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
⁴ Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: [email protected].

Abstract

Single-cell sequencing is a powerful technology to understand the heterogeneity of clinical biospecimens. Here, we present a protocol for obtaining single-cell suspension from neurofibromatosis type 1-associated nerve sheath tumors for transcriptomic profiling on the 10x platform. We describe steps for clinical sample collection, generation of single-cell suspension, and cell capture and sequencing. We then detail methods for integrative analysis, developmental Schwann cell trajectory building using bioinformatic tools, and comparative analysis. This protocol can be adapted for single-cell sequencing using mouse nerve tumors. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2022).¹.

Keywords: Bioinformatics; Cancer; Genetics; RNAseq; Single Cell.

Published by Elsevier Inc.