Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide profiling at single-nucleotide resolution of brain cell types in schizophrenia [WGBS]

ABSTRACT: Genome-wide profiling at single-nucleotide resolution of brain cell types in schizophrenia [WGBS]

PROVIDER: PRJNA421218 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6373900_1.fastq.gz	Fastqsanger.gz
	SRR6373900_2.fastq.gz	Fastqsanger.gz
	SRR6373910_1.fastq.gz	Fastqsanger.gz
	SRR6373910_2.fastq.gz	Fastqsanger.gz
	SRR6373920_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 364

Similar Datasets

Genome-wide profiling at single-nucleotide resolution of brain cell types in schizophrenia [WGBS]

Project description:We carried out cell-type specific whole genome bisulfite sequencing from BA46 that underwent fluorescence-activated nuclei sorting (FANS).

2019-06-25 | GSE107729 | GEO

DNA methylation in schizophrenia in different patient-derived cell types

Project description:DNA methylation of gene promoter regions represses transcription and is a mechanism via which environmental risk factors could affect cells during development in individuals at risk for schizophrenia. We investigated DNA methylation in patient-derived cells that might shed light on early development in schizophrenia. Induced pluripotent stem cells (iPS cells) may reflect a âground stateâ upon which developmental and environmental influences would be minimal. Olfactory neurosphere-derived cells (ONS cells) are an adult-derived neuro-ectodermal stem cell modified by developmental and environmental influences. Fibroblasts provide a non-neural control for life-long developmental and environmental influences. Genome-wide profiling of DNA methylation and gene expression was done in these three cell types from the same individuals. All cell types had distinct, statistically significant schizophrenia-associated differences in DNA methylation and linked gene expression, with Gene Ontology analysis showing that the differentially affected genes clustered in networks associated with cell growth, proliferation and movement, functions known to be affected in schizophrenia patient-derived cells. Only 5 gene loci were differentially methylated in all three cell types. These findings suggest that schizophrenia-associated DNA methylation may be a response to the homeostatic demands of different cell types in their local environments. Understanding the role of epigenetics in cell function in the brain in schizophrenia is likely to be complicated by similar cell type differences in intrinsic and environmentally-induced epigenetic regulation. This dataset represents the gene expression part of the study. The DNA methylation data is deposited under accession E-MTAB-2154.

2017-11-01 | E-MTAB-5016 | biostudies-arrayexpress

Individual nucleotide resolution Crosslinking Immunoprecipitation (iCLIP)-seq

Project description:Individual nucleotide resolution Crosslinking Immunoprecipitation (iCLIP)-seq

| PRJNA564016 | ENA

Single-nucleotide-resolution mapping of HBV promoters using CAGE

Project description:We provide a comprehensive map of transcription start sites (TSSs) for HBV at single nucleotide resolution using CAGE.

2016-09-16 | GSE84186 | GEO

Contribution of differential cell-specific methylation to schizophrenia [RNA-seq]

Project description:To address the heterogeneity of gene regulation and expression in cell types of a brain region with strong evidence for relevance to schizophrenia, we carried out whole genome methylation and expression analyses using post-mortem brain tissue from BA46 that underwent fluorescence-activated nuclei sorting (FANS). Importantly, we used whole genome bisulfite sequencing (WGBS) for methylation quantification to have an unbiased assessment of epigenetic modifications associated with schizophrenia, and additionally carried out whole genome sequencing (WGS) of the brain samples to account for genetic background differences. We found that a number of schizophrenia GWAS loci overlap with sites of cell-specific differential methylation in schizophrenia brain tissue. Differential methylation is also associated with differential gene expression in a cell-specific manner. Co-expression network analysis can identify groups of genes that are enriched for differentially methylated regions in each cell type, and these groups of co-expressed genes underscore shared molecular pathways that might be at risk in schizophrenia. Together, these data indicate that the integration of multiple levels of data in a cell-specific manner can provide novel biological insights into complex genetic disorders such as schizophrenia.

2019-06-25 | GSE107638 | GEO

12 single-base resolution methylomes of three life stages using WGBS

Project description:As the most studied type of epigenetic modifications found in many taxa, DNA methylation has been confirmed to play a crucial role in transposon silencing, transcriptional regulation and thus phenotypic variation, as well as rapid adaption to changing environments. To fully understand the methylome variation in Trichinella, here, we report 12 single-base resolution methylomes of three life stages using WGBS. By comparative epigenomics, we observe that the methylome variation in Trichinella is significantly divergent and host-related. By comparative epigenomics, we observe that the methylome variation in Trichinella is significantly divergent and host-related. By comparing DNA methylation patterns between different host classes of species, we found a fraction of parasitism-related genes under epigenetic regulation, such as G-protein-coupled receptor, DNaseII and ligand-gated chloride channel. Moreover, we also reveal associations between methylation divergence and genetic basis, including nucleotide variant and structural variation.

2021-06-01 | GSE139486 | GEO

Nucleotide resolution genome-wide mapping of 8-oxoG damage

Project description:Nucleotide resolution genome-wide mapping of 8-oxoG damage

| PRJNA445275 | ENA

Single-nucleotide-resolution mapping of HBV promoters using CAGE

Project description:Single-nucleotide-resolution mapping of HBV promoters using CAGE

| PRJNA328244 | ENA

Single Nucleotide Resolution Analysis of Nucleotide Excision Repair of Ribosomal DNA in Humans and Mice

Project description:Single Nucleotide Resolution Analysis of Nucleotide Excision Repair of Ribosomal DNA in Humans and Mice

| PRJNA495394 | ENA

Schizophrenia Proteome Data High Resolution Method

Project description:PTM-tolerant quantitative proteome analysis of plasma collected from schizophrenia patients and nonspychiatric healthy controls.

2021-03-02 | MSV000086977 | MassIVE

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