Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data

Aizhan Surumbayeva; Michael Kotliar; Linara Gabitova-Cornell; Andrey Kartashov; Suraj Peri; Nathan Salomonis; Artem Barski; Igor Astsaturov

doi:10.1016/j.xpro.2021.100989

Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data

STAR Protoc. 2021 Dec 4;2(4):100989. doi: 10.1016/j.xpro.2021.100989. eCollection 2021 Dec 17.

Authors

Aizhan Surumbayeva¹, Michael Kotliar^{2

3}, Linara Gabitova-Cornell¹, Andrey Kartashov^{2

3

4}, Suraj Peri^{5

6}, Nathan Salomonis^{7

3}, Artem Barski^{2

8

3

4}, Igor Astsaturov^{1

6}

Affiliations

¹ The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
² Division of Allergy and Immunology, University of Cincinnati, Cincinnati, OH 45221, USA.
³ Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45221, USA.
⁴ Datirium, LLC, Cincinnati, OH 45226, USA.
⁵ Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
⁶ Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
⁷ Division of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45221, USA.
⁸ Division of Human Genetics, University of Cincinnati, Cincinnati, OH 45221, USA.

Abstract

Preparation of single-cell suspension from primary tumor tissue can provide a valuable resource for functional, genetic, proteomic, and tumor microenvironment studies. Here, we describe an effective protocol for mouse pancreatic tumor dissociation with further processing of tumor suspension for single-cell RNA sequencing analysis of cellular populations. We further provide an outline of the bioinformatics processing of the data and clustering of heterogeneous cellular populations comprising pancreatic tumors using Common Workflow Language (CWL) pipelines within user-friendly Scientific Data Analysis Platform (https://SciDAP.com). For complete details on the use and execution of this protocol, please refer to Gabitova-Cornell et al. (2020).

Keywords: Bioinformatics; Cancer; Cell Biology; Cell isolation; Molecular Biology; RNAseq; Sequence analysis; Single Cell.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Computational Biology / methods*
Female
Male
Mice
Pancreas / cytology
Pancreas / pathology
Pancreatic Neoplasms* / genetics
Pancreatic Neoplasms* / metabolism
Pancreatic Neoplasms* / pathology
Sequence Analysis, RNA / methods*
Single-Cell Analysis / methods*
Software

Grants and funding

R41 HG011219/HG/NHGRI NIH HHS/United States