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

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

PROVIDER: PRJNA454443 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7088030.fastq.gz	Fastqsanger.gz
	SRR7088031.fastq.gz	Fastqsanger.gz
	SRR7088032.fastq.gz	Fastqsanger.gz
	SRR7088033.fastq.gz	Fastqsanger.gz
	SRR7088034.fastq.gz	Fastqsanger.gz

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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

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 (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 (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

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-11-15 | GSE113673 | GEO

Single-nucleus RNA-sequencing of plants

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Single-nucleus total RNA-sequencing of C2C12 myoblasts via in situ polyadenylation

Project description:Current methods for single-nucleus RNA-sequencing (snRNAseq) are limited to assaying endogenously polyadenylated (A-tailed) RNA transcripts. Here we demonstrate that enzymatic in situ polyadenylation of RNAs enables detection of the full spectrum of RNAs, expanding the scope of sequencing-based single-nucleus transcriptomics to the total transcriptome. We apply standard snRNAseq and total snRNAseq to C2C12 myoblasts. Our in situ polyadenylation strategy relies on a brief, low-cost add-on to a widely used protocol for single-cell/single-nucleus RNA-sequencing, and thus could be broadly and quickly adopted. Single-nucleus RNA-sequencing of the total transcriptome will enable new insights into gene regulation and biology.

2022-08-01 | GSE209780 | GEO

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