Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic profiling of esophageal epithelium reveals enrichment of IFN-γ response gene signature during active EoE.

ABSTRACT: Transcriptomic profiling of esophageal epithelium reveals enrichment of IFN-γ response gene signature during active EoE.

PROVIDER: PRJNA983824 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR24919615_1.fastq.gz	Fastqsanger.gz
	SRR24919615_2.fastq.gz	Fastqsanger.gz
	SRR24919616_1.fastq.gz	Fastqsanger.gz
	SRR24919616_2.fastq.gz	Fastqsanger.gz
	SRR24919617_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 46

Similar Datasets

Transcriptomic profiling of esophageal epithelium reveals enrichment of IFN-γ response gene signature during active EoE.

Project description:Eosinophilic esophagitis (EoE) is a chronic, allergic inflammatory disease of the esophageal mucosa. Although type 2 cytokines are predominant, targeting type 2 inflammation alone is not always effective for all patients. In EoE patients, the transcriptional profiling of esophageal biopsy reveals upregulation of type I and II interferon (IFN) response, dysregulated immune signaling, and downregulation of esophageal-specific genes. However, further investigation is needed to examine the gene expression changes in esophageal epithelium because it plays an important role in EoE. To investigate the upregulation of Interferon Stimulated Genes (ISGs) in EoE esophageal epithelium, we isolated epithelial cells from active EoE patients and non-EoE controls. We performed bulk RNA sequencing to analyze the epithelial-specific transcriptome in EoE. Unsupervised hierarchical clustering of the most variable genes differentiated the active EoE biopsies from non-EoE controls. Gene set enrichment analysis identified IFN-γ response as the most significant upregulated pathway.

2024-02-26 | GSE234973 | GEO

Effect of IFN-α and IFN-γ on gene expression of 3D organoids derived from telomerase-immortalized normal human esophageal keratinocyte cell line, EPC2-hTERT.

Project description:Eosinophilic esophagitis (EoE) is a chronic, allergic inflammatory disease of the esophageal mucosa. While type 2 cytokines are predominant, targeting type 2 inflammation alone is not always effective for all patients. In EoE patients, the transcriptional profiling of esophageal biopsy reveal upregulation of type I and II interferon (IFN) response, dysregulated immune signaling and downregulation of esophageal-specific genes in EoE patients. However, the role of interferon signaling during EoE is not fully understood. This study aims to investigate the impact of IFN signaling on esophageal epithelium and elucidate its role in EoE. IFN-γ stimulation of esophageal epithelial cells triggered disruption of tissue differentiation, epithelial barrier integrity and cytotoxicity, which are relevant features of EoE immunopathology. Beyond EoE, our findings offer insights into esophageal disorders which may involve increased IFN-γ signaling, including infections, gastrophageal reflux disease, and Barrett's esophagus.

2024-02-26 | GSE234424 | GEO

The EoE esophageal epithelial transcriptomic landscape

Project description:We report alterations in the esophageal transcriptome of adult eosinophilic esophagitis (EoE) patients at a single-cell transcriptomic level.

2023-08-07 | GSE218607 | GEO

The EoE esophageal epithelial transcriptomic landscape

Project description:The EoE esophageal epithelial transcriptomic landscape

| PRJNA904499 | ENA

Amphiregulin-producing T helper 2 cells have critical role in esophageal fibrosis of EoE

Project description:Background: Massive eosinophil infiltration into the esophagus causes subepithelial fibrosis and esophageal stricture in patients with eosinophilic esophagitis (EoE). However, the pathogenesis of esophageal fibrosis remains unclear. Objective: The present study aimed to elucidate the cellular and molecular mechanisms underlying the induction of esophageal fibrosis. Methods: We established a murine model of EoE accompanied by fibrotic responses following long-term intranasal administration of house dust mite (HDM) antigen. Using this murine model, we investigated the characteristics of immune cells infiltrating the fibrotic region of the inflamed esophagus using flow cytometry and histological analyses. We also analyzed the local inflammatory sites in the esophagus of patients with EoE using single-cell RNA sequencing, flow cytometry, and immunohistochemistry.

2024-08-05 | GSE249276 | GEO

Genome wide expression from esophageal biopsies of subjects with EoE-like inflammatory diseases, eosinophilic esophagitis, gastroesophageal reflux disease and healthy controls

Project description:Esophageal biopsy RNA was isolated from proximal esophageal biopsied RNA from patients with EoE-like inflammatory diseases (EoE-like esophagitis, lymphocytic esophagitis, non-specific esophagitis), patients with active EoE, patients with GERD, and unaffected healthy controls. EoE-like inflammatory disease patients were clinically active at the time when biopsies were taken. None of the patients (EoE-like inflammatory diseases, EoE, GERD and controls) were under anti-eosinophil treatment (including dietary restrictions). The quality of the RNA-seq data was assessed using fastqc v. 0.11.5 1) and RSeQC v. 2.6.4 2). The reads were mapped to the reference genome using HiSat2 v. 2.1.0 3). FeatureCounts v. 1.6.0 4) was used to count the number of reads overlapping with each gene as specified in the genome annotation (Homo_sapiens.GRCh38.94). The Bioconducture package DESeq2 5) was used to test for differential gene expression between the experimental groups. TopGo 6) was used to identify gene ontology terms containing unusually many differentially expressed genes. An interactive Shiny application was set up to facilitate the exploration and visualisation of the RNA-seq results. All analyses were run in R version 3.4.4 (2018-03-15)

2022-02-28 | GSE148381 | GEO

Single-cell RNA Sequencing of Human Esophageal Epithelium in Homeostasis and Allergic Inflammation

Project description:To investigate gene expression signature of the human esophageal epithelium at the homeostatic and inflammatory conditions we performed scRNAseq on the human esophageal biopsies obtained from the healhy patients, patients with active eosinophilic esophagitis (EoE) and patients in the remission.

2022-06-15 | GSE201153 | GEO

Novel genes differentiating Eosinophilic Esophagitis (EoE) from GERD identified by RNA Sequencing

Project description:RNA sequencing analysis of proximal and distal esophageal biopsies from a small cohort of EoE, GERD, and control patients was performed to identify differentially expressed genes.

2018-12-31 | GSE41687 | GEO

Proteomic Analysis of Eosinophilic Esophagitis: Identification and Involvement of the Minichromosome Maintenance Complex as a Driver of Esophageal Basal Zone Hyperplasia

Project description:To uncover molecular drivers of Eosinophilic Esophagitis (EoE), a global proteome screen of the esophageal biopsies from individuals with and without EoE was performed.

2023-08-01 | PXD040030 | Pride

PolyA RNA-seq from Human esophageal biopsy samples from eosinophilic esophagitis patients

Project description:Analysis of steady-state mRNA levels in 27 samples from healthy controls and patients with fibrostenotic EoE and non-fibrostenotic EoE. Participants range 5 – 18 years old. EoE participants had >15 eosinophils per hpf (eos/hpf) and were classified as fibrostenotic (FS) or non-fibrostenotic (non-fs). FS EoE: having either a) a stricture and/or b) grade 2 or 3 concentric esophageal rings and an esophageal distensibility < 15 mm. Non-fs EoE: no clinical evidence for stricture, circumferential rings or history of food impaction. Included control subjects had no identified abnormalities on endoscopy or histology. Results provide insight into the pathways involved in fibrostenotic remodeling in EoE.

2023-04-08 | GSE197702 | GEO

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