Detecting microRNA-mediated gene regulatory effects in murine neuronal subpopulations

Neal D Amin; Gokhan Senturk; Marito Hayashi; Shawn P Driscoll; Samuel L Pfaff

doi:10.1016/j.xpro.2022.101130

Detecting microRNA-mediated gene regulatory effects in murine neuronal subpopulations

STAR Protoc. 2022 Jan 25;3(1):101130. doi: 10.1016/j.xpro.2022.101130. eCollection 2022 Mar 18.

Authors

Neal D Amin¹, Gokhan Senturk¹, Marito Hayashi¹, Shawn P Driscoll¹, Samuel L Pfaff¹

Affiliation

¹ Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines, La Jolla, CA 92037, USA.

Abstract

microRNAs (miRNAs) have unique gene regulatory effects in different neuronal subpopulations. Here, we describe a protocol to identify neuronal subtype-specific effects of a miRNA in murine motor neuron subpopulations. We detail the preparation of primary mouse spinal tissue for single cell RNA sequencing and bioinformatics analyses of pseudobulk expression data. This protocol applies differential gene expression testing approaches to identify miRNA target networks in heterogeneous neuronal subpopulations that cannot otherwise be captured by bulk RNA sequencing approaches. For complete details on the use and execution of this protocol, please refer to Amin et al. (2021).

Keywords: Bioinformatics; Cell isolation; Developmental biology; Flow Cytometry/Mass Cytometry; Gene Expression; Model Organisms; Neuroscience; Single Cell.

Publication types

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

MeSH terms

Animals
Computational Biology / methods
Gene Expression Regulation
Mice
MicroRNAs* / genetics
Neurons
Sequence Analysis, RNA

Substances

MicroRNAs