UMB Data Catalog

A project of the Health Sciences and Human Services Library
UMB Dataset

Single-Nucleus RNA-Seq Reveals Dysregulation of Striatal Cell Identity Due to Huntington’s Disease Mutations

UID: 204
Author(s): Sonia Malaiya, Marcia Cortes-Gutierrez, Brian R. Herb, Sydney R. Coffey, Samuel R. W. Legg...
* Corresponding Author
Description
The involvement of specific medium spiny neuro (MSN) subtype and of other striatal cell types remains poorly understood. To gain insight into cell type-specific disease processes, researchers studied the nuclear transcriptomes of 4524 cells from the striatum of a genetically precise knock-in mouse model of the Huntington's Disease (HD) mutation, HttQ175/1. Three 14-month-old and one 15-month-old male mice were used to generate the primary dataset.
Timeframe
2020
Geographic Coverage
Ethiopia
Subject of Study
Subject Domain
Sequence Analysis, RNA
Subject Gender
Male
Keywords
Huntington Disease/genetics
Medium Spiny Neurons/pathology

Access

Restrictions
Unrestricted access
Instructions
Access data via article and the Gene Expression Analysis Resources
Access via Article

Data tables and figures

Access via Gene Expression Analysis Resource

Gene expression visualization and analysis

Associated Publications
Malaiya S, Cortez-Gutierrez M, Herb BR, Coffey SR, Legg SRW, Cantle JP, Colantuoni C, Carroll JB, Ament SA.Single-Nucleus RNA-Seq Reveals Dysregulation of Striatal Cell Identity Due to Huntington’s Disease Mutations. J. Neurosci. 2021 June 23;41(25):5534-5552
Data Type
Genomic
Equipment Used
BioPulverizer

fragments hard frozen tissue samples into tiny pieces

MoxiGo cytometer

rapid multi-parametric analysis of single cells in solution

Software Used
Chromium Single Cell Gene expression 3

sequence samples

GENIE3

inferring gene regulatory networks from expression data

limma

data analysis, linear models and differential expression for microarray data

RRHO

algorithm that allows for the comparison of two gene expression signatures

Seurat v3.0 R

QC, analysis, and exploration of single-cell RNA-seq data

SoupX

removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

Study Type
Observational
Dataset Format(s)
Microsoft Excel
Dataset Size
24MB
Grant Support
R24 MH114815/BRAIN Initiative