Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

EGAS00001003519-sc-2021-09-02T08:18:51Z - samples

ABSTRACT: The dataset comprises of 5' single cell RNA sequencing with TCR enrichment with 10x Genomics' Chromium technology of multiregional biopsies of human renal cell carcinomas. Biopsies from different tumour regions, the tumour-normal interface, normal kidney, normal adrenal, metastatic regions, peri-nephric fat, and peripheral blood were sequenced from 12 patients with kidney tumours.

PROVIDER: EGAD00001008030 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Methylome analysis of normal kidney, nephrogenic rest and Wilms tumor

Project description:Genome wide DNA methylation profiling of normal kidney (n=36), nephrogenic rest (n=22) and Wilms tumour (n=37) was performed using the Illumina 450k array. Two papers were composed after analysis of this data (1) describes comparative analysis of 22 matched normal kidney-Wilms tumour pairs which identified biomarker differentially methylated regions (DMRs) that could be detected in patient blood; (2) describes comparative analysis of 20 matched trios which identified changes in methylation associated with progression from the precursor lesion towards tumourigenesis. Bisulfte converted DNA from 95 samples of normal kidney, nephrogenic rest and Wilms tumour was hybridised to Illumina HumanMethylation450 bead chips.

2014-07-08 | E-GEOD-59157 | biostudies-arrayexpress

Methylome analysis of normal kidney, nephrogenic rest and Wilms tumor

2014-07-08 | GSE59157 | GEO

Glioblastoma intra-tumour transcriptomics

Project description:Gene expression microarray profiling on glioblastoma intra-tumour regions, where the study hypothesis states that the infiltrative tumour margin harbours a distinct transcriptomic profile from all non-infiltrative tumour regions. Data is from three patients (patient 9, 14 and 15) where regions 1-4 per patient were obtained from non-infiltrative intra-tumour regions, and region 5 was obtained from the infiltrative margin. All patients underwent craniotomy with intra-operative image guidance and visualization of 5ALA induced fluorescence to obtain infiltrative margin biopsies.

2024-11-30 | E-MTAB-14600 | biostudies-arrayexpress

The spatially resolved transcriptional profile of acute T cell-mediated rejection in a kidney allograft

Project description:Herein, we used the whole exome GeoMX Digital Space Profiling platform to study five tubular and three glomerular regions of interest in the kidney graft biopsy from a patient with a chronic-active TCMR episode and in analogous areas from two different normal kidney control biopsies. All kidney sections were from paraffin blocks. Overall, inflammatory genes were significantly upregulated in the tubular areas of the TCMR biopsy and showed an enrichment for gene-ontology terms associated with T-cell activation, differentiation, and proliferation. Enrichment analysis of the 100 genes with the highest coefficient of variation across the TCMR tubular regions of interest revealed that these highly variable genes are involved in kidney development and injury and interestingly do not associate with the 2019 Banff classification pathology scores within the individual regions of interest. Spatial transcriptomics allowed us to unravel a previously unappreciated variability across different areas of the TCMR biopsy related to the graft response to the alloimmune attack, rather than to the immune cells

2024-11-05 | GSE281078 | GEO

Pre transplantation Kidney Biopsies

Project description:Pre transplantation Kidney Biopsies

| PRJNA888648 | ENA

Involvement of NK cells and Fc gamma receptors in different kidney allograft rejection types

Project description:To investigate the involvement of FCGR3A and FCGR2C signaling and NK cell activation during antibody-mediated rejection, we analyzed transcriptomic data obtained by bulk RNA sequencing of kidney allograft FFPE biopsies diagnosed with either antibody-mediated rejection, T-cell mediated rejection or normal biopsies.

2024-12-01 | GSE214703 | GEO

High-fat diet fuels prostate cancer progression by rewiring the metabolome and amplifying the MYC program

Project description:Systemic metabolic alterations associated with increased consumption of saturated fat and obesity are linked with increased risk of prostate cancer progression and mortality, but the molecular underpinnings of this association are poorly understood. Here, we demonstrate in a murine prostate cancer model, that high-fat diet (HFD) enhances the MYC transcriptional program through metabolic alterations that favour histone H4K20 hypomethylation at the promoter regions of MYC regulated genes, leading to increased cellular proliferation and tumour burden. Saturated fat intake (SFI) is also associated with an enhanced MYC transcriptional signature in prostate cancer patients. The SFI-induced MYC signature independently predicts prostate cancer progression and death. Finally, switching from a high-fat to a low-fat diet, attenuates the MYC transcriptional program in mice. Our findings suggest that in primary prostate cancer, dietary SFI contributes to tumour progression by mimicking MYC over expression, setting the stage for therapeutic approaches involving changes to the diet.

2019-08-22 | MTBLS135 | MetaboLights

Transvaginal Versus Transabdominal Extraction of Laparoscopically-excised Specimen

Project description:The aim of this study is to evaluate the outcomes of transvaginal natural orifice specimen extraction (NOSE) in patients who are planning multiport laparoscopic surgery for resection of solid organs including kidney, liver, stomach, adrenal gland and bladder.

| 2394936 | ecrin-mdr-crc

Correlation of Survival with Gene Expression in Oesophageal Cancer

Project description:We evaluated and correlated gene expression profiles of pre-treatment endoscopic biopsies in a pre-defined patient population of resectable oesophageal adenocarcinoma who had received neoadjuvant platinum and fluoropyrimidine based chemotherapy with clinical outcome, the primary end-point being overall survival. At the time of pre-treatment staging EUS, tumour biopsies were collected (approximately 1.5 mm3). and immediately snap frozen and stored in liquid nitrogen. Total RNA was extracted from the biopsies and amplified using a T7 bacteriophage RNA polymerase based linear amplification protocol, then expression profiling was carried out. The expression levels of 47 genes selected by biological function, fold change and degree of significance were further validated using quantitative reverse transcription-PCR Keywords: Tumour vs normal comparison

2008-08-15 | GSE11595 | GEO

circRNA-sequencing

Project description:We aim to identify profiling of circRNAs in renal biopsies from lupus nephritis (LN) patients. In this study, seven frozen renal biopsies from patients with LN class IV were used for circRNA profiling by second generation of RNA sequencing. Three kidney tissue 5 cm far from renal tumors were used as normal control .

2020-12-16 | GSE108340 | 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