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

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

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

3 Scopus citations

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).

Original language	English
Article number	100989
Pages (from-to)	100989
Journal	STAR Protocols
Volume	2
Issue number	4
DOIs	https://doi.org/10.1016/j.xpro.2021.100989
State	Published - Dec 17 2021

Keywords

Animals
Computational Biology/methods
Female
Male
Mice
Pancreas/cytology
Pancreatic Neoplasms/genetics
Sequence Analysis, RNA/methods
Single-Cell Analysis/methods
Software
Molecular Biology
Cell isolation
RNAseq
Cell Biology
Single Cell
Bioinformatics
Sequence analysis
Cancer

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10.1016/j.xpro.2021.100989

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title = "Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data",

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 = "Animals, Computational Biology/methods, Female, Male, Mice, Pancreas/cytology, Pancreatic Neoplasms/genetics, Sequence Analysis, RNA/methods, Single-Cell Analysis/methods, Software, Molecular Biology, Cell isolation, RNAseq, Cell Biology, Single Cell, Bioinformatics, Sequence analysis, Cancer",

author = "Aizhan Surumbayeva and Michael Kotliar and Linara Gabitova-Cornell and Andrey Kartashov and Suraj Peri and Nathan Salomonis and Artem Barski and Igor Astsaturov",

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year = "2021",

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doi = "10.1016/j.xpro.2021.100989",

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AU - Surumbayeva, Aizhan

AU - Kotliar, Michael

AU - Gabitova-Cornell, Linara

AU - Kartashov, Andrey

AU - Peri, Suraj

AU - Salomonis, Nathan

AU - Barski, Artem

AU - Astsaturov, Igor

PY - 2021/12/17

Y1 - 2021/12/17

N2 - 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).

AB - 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).

KW - Animals

KW - Computational Biology/methods

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KW - Male

KW - Mice

KW - Pancreas/cytology

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KW - Sequence Analysis, RNA/methods

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JO - STAR Protocols

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

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

Abstract

Keywords

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Biological Imaging Facility

Biostatistics and Bioinformatics Facility

Laboratory Animal Facility

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