Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases

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

ORGANISM(S): Homo sapiens

PROVIDER: GSE185941 | GEO | 2022/11/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [HiChIP]

Project description:30 B-lymphoblastoid cell lines (LCLs) with genome-wide genotype data were treated with hydrocortisone (GR agonist) and CORT108297 (GR modulator), followed by RNA-seq to identify PGx-eQTLs. We then integrated GR chromatin immunoprecipitation-sequencing (ChIP-seq) to characterize the epigenetic function of PGx-eQTLs that interfere with GR response elements. We also applied a high-throughput enhancer assay (STARR-seq) using PGx-eQTL loci DNA sequences to “scan” for drug-dependent SNPs.

2022-11-16 | GSE189453 | GEO

Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [STARR-seq]

2022-11-16 | GSE185939 | GEO

Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [ChIP-seq]

2022-11-16 | GSE185928 | GEO

Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [RNA-seq]

2022-11-16 | GSE185908 | GEO

Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases

Project description:Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases

| PRJNA771402 | ENA

Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [HiChIP]

Project description:Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [HiChIP]

| PRJNA783038 | ENA

Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [RNA-seq]

Project description:Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [RNA-seq]

| PRJNA771341 | ENA

Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [ChIP-seq]

Project description:Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [ChIP-seq]

| PRJNA771385 | ENA

Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [STARR-seq]

Project description:Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [STARR-seq]

| PRJNA771405 | ENA

Genetic Risk Variants for Autoimmune Diseases that Influence Gene Expression in Thymus

Project description:Genome-wide association studies (GWAS) have boosted our knowledge of genetic risk variants in autoimmune diseases (AIDs). Most of the risk variants are located within or near genes with immunological functions, and the majority is found to be non-coding, pointing towards a regulatory role. We have performed a cis expression quantitative trait locus (eQTL) screen to investigate whether single nucleotide polymorphisms (SNPs) associated with AIDs influence gene expression in thymus. Genotyping was performed using the Immunochip and 353 AID associated SNPs were tested against expression of surrounding genes (+/- 1 Mb) from human thymic tissue (N=42). We identified eight genes where the expression was associated with AID risk SNPs at a study-wide level of significance (P < 2.57x10-5). Five genes (FCRL3, RNASET2, C2orf74, SIRPG and SYS1) displayed cis eQTL signals also in other tissues, while for two loci (NPIPB8 and LOC388814), the eQTL signal appear to be thymus-specific. Since many AID risk variants from GWAS have been subsequently fine-mapped in recent Immunochip projects, we explored the overlap between these novel AID risk variants and the thymic eQTL regions. Moreover, we examined the functional annotation of the seven expression altering SNPs (eSNPs). Our study reveals autoimmune risk variants that act as eQTLs in thymus. We have highlighted functional variants within these genetic regions that potentially can represent causal autoimmune risk variants. Total RNA from 42 human thymic samples were obtained from children undergoing cardiac surgery.

2016-01-21 | E-GEOD-77052 | 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