Dataset Information

Single-Cell Isolation from Regenerating Murine Muscles for RNA-Sequencing Analysis.

ABSTRACT: Single-cell RNA sequencing (scRNA-seq) is a powerful technique for deconvoluting and clustering thousands of otherwise intermingled cells based on their gene expression. Here, we present a complete protocol for the unbiased evaluation of regenerating murine skeletal muscle using scRNA-seq. The skeletal muscle is unique in its cellular composition as being primarily multinucleated muscle cells (myofibers). This protocol focuses on isolating mononuclear cells from muscle for subsequent scRNA-seq analysis and can be modified to assess cell populations in other tissues of interest. For complete details on the use and execution of this protocol, please refer to Liu et al. (2015) and Oprescu et al. (2020).

SUBMITTER: Oprescu SN

PROVIDER: S-EPMC7580090 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Publications

Single-Cell Isolation from Regenerating Murine Muscles for RNA-Sequencing Analysis.

Oprescu Stephanie N SN Yue Feng F Kuang Shihuan S

STAR protocols 20200612 2

Single-cell RNA sequencing (scRNA-seq) is a powerful technique for deconvoluting and clustering thousands of otherwise intermingled cells based on their gene expression. Here, we present a complete protocol for the unbiased evaluation of regenerating murine skeletal muscle using scRNA-seq. The skeletal muscle is unique in its cellular composition as being primarily multinucleated muscle cells (myofibers). This protocol focuses on isolating mononuclear cells from muscle for subsequent scRNA-seq a ...[more]

PMID: 33111097

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Project description:The advent of single-cell RNA sequencing (scRNA-Seq) has brought with it the ability to gain greater insights into the cellular composition of tissues and heterogeneity in gene expression within specific cell types. For tissue-engineered blood vessels, this is particularly impactful to better understand how neotissue forms and remodels into tissue resembling a native vessel. A notable challenge, however, is the ability to separate cells from synthetic biomaterials to generate high-quality single-cell suspensions to interrogate the cellular composition of our tissue-engineered vascular grafts (TEVGs) during active remodeling in situ. We present here a simple, commercially available approach to separate cells within our TEVG from the residual scaffold for downstream use in a scRNA-Seq workflow. Utilizing this method, we identified the cell populations comprising explanted TEVGs and compared these with results from immunohistochemical analysis. The process began with explanted TEVGs undergoing traditional mechanical and enzymatic dissociation to separate cells from scaffold and extracellular matrix proteins. Magnetically labeled antibodies targeting murine origin cells were incubated with enzymatic digests of TEVGs containing cells and scaffold debris in suspension allowing for separation by utilizing a magnetic separator column. Single-cell suspensions were processed through 10 × Genomics and data were analyzed utilizing R to generate cell clusters. Expression data provided new insights into a diverse composition of phenotypically unique subclusters within the fibroblast, macrophage, smooth muscle cell, and endothelial cell populations contributing to the early neotissue remodeling stages of TEVGs. These populations were correlated qualitatively and quantitatively with immunohistochemistry highlighting for the first time the potential of scRNA-Seq to provide exquisite detail into the host cellular response to an implanted TEVG. These results additionally demonstrate magnetic cell isolation is an effective method for generating high-quality cell suspensions for scRNA-Seq. While this method was utilized for our group's TEVGs, it has broader applications to other implantable materials that use biodegradable synthetic materials as part of scaffold composition. Impact statement Single-cell RNA sequencing is an evolving technology with the ability to provide detailed information on the cellular composition of remodeling biomaterials in vivo. This present work details an effective approach for separating nondegraded biomaterials from cells for downstream RNA-sequencing analysis. We applied this method to implanted tissue-engineered vascular grafts and for the first time describe the cellular composition of the remodeling graft at a single-cell gene expression level. While this method was effective in our scaffold, it has broad applicability to other implanted biomaterials that necessitate separation of cell from residual scaffold materials for single-cell RNA sequencing.

Dataset Information

Single-Cell Isolation from Regenerating Murine Muscles for RNA-Sequencing Analysis.

Publications

Single-Cell Isolation from Regenerating Murine Muscles for RNA-Sequencing Analysis.

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