Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single Cell RNA sequencing (DropSeq) of esophageal adenocarcinoma and matched normal samples

ABSTRACT: Single Cell RNA sequencing (DropSeq) of esophageal adenocarcinoma and matched normal samples

PROVIDER: PRJNA727596 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR14447348_1.fastq.gz	Fastqsanger.gz
	SRR14447348_2.fastq.gz	Fastqsanger.gz
	SRR14447349_1.fastq.gz	Fastqsanger.gz
	SRR14447349_2.fastq.gz	Fastqsanger.gz
	SRR14447350_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 158

Similar Datasets

Single Cell RNA sequencing (DropSeq) of esophageal adenocarcinoma and matched normal samples

Project description:Cancer grows within the complex ecosystem of the tumor microenvironment (TME) which can define responses to treatment. Esophageal adenocarcinoma (EAC) is typically resistant to cytotoxic therapies and immunotherapies have gained little traction against this disease. We used single cell RNA sequencing to identify the key constituents of the TME in EAC in a cohort of 22 patients. We found differences within and between individual patients in cancer cells and also in the stromal and immune cell populations. We found a subtype of cancer-associated fibroblasts, the myofibroblastic CAFs (myoCAFs), acting as TME interaction hubs to drive the hallmarks of cancer. Finally, we demonstrated the efficacy of repurposed PDE5 inhibitors in targeting myoCAFs in near-patient models of the disease.

2021-05-06 | GSE173950 | GEO

Esophageal Adenocarcinoma

Project description:Esophageal Adenocarcinoma

| PRJNA188928 | ENA

Esophageal adenocarcinoma

Project description:Esophageal adenocarcinoma

| PRJNA1072671 | ENA

miR-223 in esophageal adenocarcinoma carcinogenesis

Project description:miR-223 is step-wise increasingly up-regulated in the normal esophagus - Barrett's esophagus -esophageal adenocarcinoma carcinoma sequence. In this study, we aimed to determine the function of miR-223 in esophageal adenocarcinoma carcinogenesis.

2013-02-07 | GSE44120 | GEO

Affymetrix SNP 6.0 data for analysis of esophageal adenocarcinoma samples

Project description:Esophageal adenocarcinoma is characterized by complex chromosomal alterations. Tumors were evaluated to identify regions of recurrent copy gains and losses and to determine the prognositic significance of the degree of segmental aneuploidy as measured by SNP array. 41 superficial esophageal adenocarcinomas were analyzed for copy number abnormalities. Matched normal lymph node tissue was used as a copy number reference.

2013-12-01 | E-GEOD-49396 | biostudies-arrayexpress

Barrett's esophageal tissues and esophageal adenocarcinoma specimens

Project description:This SuperSeries is composed of the following subset Series: GSE37200: Gene expression profiling of Barrett’s esophageal tissues and esophageal adenocarcinoma specimens GSE37201: Gene expression profiling of esophageal adenocarcinoma Refer to individual Series

2012-04-10 | E-GEOD-37203 | biostudies-arrayexpress

Gastric adenocarcinoma of fundic gland type vs matched normal mucosa

Project description:Gastric adenocarcinoma of fundic gland type vs matched normal mucosa

| PRJNA771083 | ENA

Integrated analysis of genome-wide copy number and matched expression data reveals novel genes in esophageal adenocarcinoma

Project description:The incidence of esophageal and junctional adenocarcinoma has increased 6-fold in the west in the last 30 years and 5 year survival remains <14%. We aimed to characterize genome-wide aberrations in esophageal adenocarcinoma to further understand disease pathogenesis and ultimately identify groups with differential survivals with implications for clinical management. Oligo-array-based high-resolution analysis of copy number changes in 89 fresh frozen esophageal adenocarcinoma resection sections with long-term clinical follow-up data was performed. Good quality array comparative genomic hybridization profiles were obtained from 56/89 of the samples (63%). Our analyses confirmed known genomic aberrations in esophageal adenocarcinoma and identified 3 novel genomic regions with copy number changes. A modified T test with adjusted Bonferroni correction identified 17 genes with significantly different log2 ratios (p<4x10-7), including 6 novel genes, that characterize a group with a poorer survival. Total DNA isolated from human tissue sections was used to make fluorescently labeled DNA that was hybridized to Illumina HumanCytoSNP-12 Beadarray. All protocols were carried out following Illumina's standard protocols. After hybridization, raw data were recorded and normalized using Illumina's BeadStudio software v2.0. Matched expression data: GSE25201 GSE19417 D2 MRC/OEA0022CJ5 (GSM482819) D3 MRC/OEA0032CJ5 (GSM482817) D27 MRC/OEA0272CJ1 (GSM482814) D36 MRC/OEA0362CJ3 (GSM482806) D37 MRC/OEA0372AJ0 (GSM482800) D96 MRC/OEA0962BJ0 (GSM482847) D118 MRC/OEA1172CJ1 (GSM482848) D138 MRC/OEA1382CJ0 (GSM482844) D156 MRC/OEA1562CJ2 (GSM482853)

2011-05-09 | E-GEOD-25201 | biostudies-arrayexpress

Multi-omic analysis of Esophageal Adenocarcinoma uncovers candidate therapeutic targets and cancer-selective post-transcriptional regulation

Project description:Efforts to address the poor prognosis associated with esophageal adenocarcinoma (EAC) have been hampered by a lack of biomarkers to identify early disease and therapeutic targets. Despite extensive efforts to understand the somatic mutations associated with EAC over the past decade, a gap remains in understanding how the atlas of genomic aberrations in this cancer impacts the proteome and which somatic variants are of importance for the disease phenotype. We performed a quantitative proteomic analysis of 23 EACs and matched adjacent normal esophageal and gastric tissues. We explored the correlation of transcript and protein abundance using tissue-matched RNAseq and proteomic data from 7 patients and further integrated these data with a cohort of EAC RNA-seq data (n=264 patients), EAC whole-genome sequencing (n=454 patients) and external published datasets.

2024-08-10 | PXD042792 | Pride

microRNA expression in Barrett's esophagus and esophageal adenocarcinoma

Project description:Barrett's esophagus is a metaplastic condition of the distal esophagus, characterized by the replacement of normal squamous epithelium by columnar epithelium. Patients with BE have an increased risk of developing esophageal adenocarcinoma. MicroRNAs have been implicated to be disease and tissue specific, however limited data of microRNA expression in the esophagus is available. Therefore we evaluated microRNA expression profiles of esophageal adenocarcinoma and compared these with Barrett's esophagus and normal squamous esophagus.

2012-03-15 | GSE29965 | 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