Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE113673 | GEO | 2018/11/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing.

Project description:In females with X-linked genetic disorders, wild-type and mutant cells coexist within brain tissue because of X-chromosome inactivation, posing challenges for interpreting the effects of X-linked mutant alleles on gene expression. We present a single-nucleus RNA sequencing approach that resolves mosaicism by using single-nucleotide polymorphisms in genes expressed in cis with the X-linked mutation to determine which nuclei express the mutant allele even when the mutant gene is not detected. This approach enables gene expression comparisons between mutant and wild-type cells within the same individual, eliminating variability introduced by comparisons to controls with different genetic backgrounds. We apply this approach to mosaic female mouse models and humans with Rett syndrome, an X-linked neurodevelopmental disorder caused by mutations in the gene encoding the methyl-DNA-binding protein MECP2, and observe that cell-type-specific DNA methylation predicts the degree of gene upregulation in MECP2-mutant neurons. This approach can be broadly applied to study gene expression in mosaic X-linked disorders.

| S-EPMC6261686 | biostudies-literature

Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing (Total RNA sequencing)

Project description:In females with X-linked genetic disorders, wild-type and mutant cells coexist within brain tissue because of random X-chromosome inactivation. This cellular mosaicism leads to phenotypic variability and poses significant challenges for interpreting the effects of X-linked mutant alleles on gene expression. We present a single-nucleus RNA sequencing approach that resolves mosaicism by using single nucleotide polymorphisms in genes that are expressed in cis with the X-linked mutation to determine whether individual nuclei express the wild-type or mutant allele even when the mutant gene is not directly detected. This approach enables genome-wide comparisons of gene expression between mutant and wild-type cells within the same individual and eliminates the variability introduced by comparisons to controls with different genetic backgrounds. We apply this approach to mosaic female mouse models and humans with Rett syndrome, an X-linked neurodevelopmental disorder caused by mutations in the methyl-DNA-binding protein MECP2, and reveal that cell-type-specific DNA methylation patterns largely predict the degree of gene upregulation by MECP2 in specific neuronal subtypes. The approach described here can be broadly applied to the characterization of gene expression in additional mosaic X-linked conditions.

2018-11-15 | GSE113902 | GEO

Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing (MeCP2 ChIP-seq)

2018-11-15 | GSE113903 | GEO

Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing (Single-cell or single-nuclei RNA sequencing)

2018-11-15 | GSE113901 | GEO

Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing

Project description:Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing

| PRJNA454441 | ENA

Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing (Total RNA sequencing)

Project description:Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing (Total RNA sequencing)

| PRJNA454443 | ENA

Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing (MeCP2 ChIP-seq)

Project description:Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing (MeCP2 ChIP-seq)

| PRJNA454444 | ENA

Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing (Single-cell or single-nuclei RNA sequencing)

Project description:Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing (Single-cell or single-nuclei RNA sequencing)

| PRJNA454442 | ENA

Protocol for single-nucleus ATAC sequencing and bioinformatic analysis in frozen human brain tissue.

Project description:Single-nucleus ATAC sequencing (snATAC-seq) employs a hyperactive Tn5 transposase to gain precise information about the cis-regulatory elements in specific cell types. However, the standard protocol of snATAC-seq is not optimized for all tissues, including the brain. Here, we present a modified protocol for single-nuclei isolation from postmortem frozen human brain tissue, followed by snATAC-seq library preparation and sequencing. We also describe an integrated bioinformatics analysis pipeline using an R package (ArchRtoSignac) to robustly analyze snATAC-seq data. For complete details on the use and execution of this protocol, please refer to Morabito et al. (2021).

| S-EPMC9218237 | biostudies-literature

Transcriptome Analysis Of Human Rett Syndrome Brain

Project description:Transcriptome analysis of postmortem brain samples frrom frontal and temporal cortex of Rett Syndrome cases and matched controls. These data identify genes differentially expressed in postmortem brain tissue from Rett Syndrome cases. Total RNA was extracted from 100mg of postmortem brain tissue.

2015-11-24 | E-GEOD-75303 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data