Kidney tumour DNA
Ontology highlight
ABSTRACT:
PROVIDER: EGAS00001002486 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:This is a bulk DNA and RNA sequencing study of human renal tumours
| EGAS00001002487 | EGA
Project description:This is an exome DNA sequencing study of human renal tumours
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Project description:This is a bulk DNA and RNA sequencing study of human renal tumours .
This dataset contains all the data available for this study on 2018-09-19.
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Project description:Multiple tumours from the same patient were analysed for DNA methylation to assess tumour clonality. Seventy-four tumours corresponding to 37 patients were stratified into four groups based on the anatomic location of the multiple breast cancers (ipsilateral or bilateral) and time interval between the diagnoses (synchronous or metachronous). Ipsilateral was defined as tumours occurring in the same breast while bilateral was defined as the occurrence of tumours in both breasts. Metachronicity was defined as a time interval greater than six months between the diagnoses of the first and second tumours, while synchronicity specified that the two tumours occurred concurrently (BM: bilateral-metachronous; BS: bilateral-synchronous; IM: ipsilateral-metachronous; IS: ipsilateral-synchronous). A subset of 16 samples was randomly selected to represent each clinical group with four samples corresponding to two patients per group and analysed for DNA methylation using Illumina Infinium Human MethylationEPIC BeadChips.
2019-01-03 | GSE108982 | GEO
Project description:DNA methylation of Human Urine Renal Progenitors after kidney transplantation
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Project description:To investigate the role of Jag1⁺ Tregs in regulating the activity of tumours and corresponding tdLNs in the B16-F10 tumour model, we performed bulk RNA sequencing on tumours and tdLNs of wild-type mice and mice with conditional deletion of Jag1 in Tregs. Transcriptomic analysis revealed no significant changes in gene expression in tumours, whereas tdLNs exhibited downregulation of lymphatic endothelial cell (LEC)-related markers and genes related to cell junction organization in mice with Treg-specific Jag1 ablation.
2026-05-18 | GSE328772 | GEO
Project description:In renal tubulointerstitial fibrosis (TIF), aberrant changes in renal drug transporters severely disrupt systemic drug disposition, leading to reduced therapeutic efficacy or increased toxicity. Although we have previously documented transporter alterations in TIF, the underlying epigenetic mechanisms remain unknown. This study aims to map the DNA methylation landscape of TIF, elucidate the epigenetic network governing transporter dysregulation, and provide mechanistic insights to support safer drug use in CKD.
2025-12-14 | E-MTAB-16261 | biostudies-arrayexpress
Project description:UHRF1 is an epigenetic regulator that plays critical roles in tumours. However, the DNA methylation alteration patterns driven by UHRF1 and the related differentially expressed tumour-related genes remain unclear. In this study, a UHRF1-shRNA MCF-7 cell line was constructed, and whole-genome bisulfite sequencing (WGBS) and RNA sequencing were performed. The DNA methylation alteration landscape was elucidated, and DNA methylation-altered regions (DMRs) were found to be distributed in both gene bodies and adjacent regions. The DMRs were annotated and categorized into 488 hypermethylated/1696 hypomethylated promoters and 1149 hypermethylated/5501 hypomethylated gene bodies. Through an integrated analysis with the RNA sequencing data, 217 upregulated methylated genes and 288 downregulated methylated genes were identified, and these genes were primarily enriched in nervous system development and cancer signalling pathways.
2024-05-09 | GSE248621 | GEO
Project description:Embryonal tumours of the central nervous system (CNS) represent a heterogeneous group of tumours about which little is known biologically, and whose diagnosis, on the basis of morphologic appearance alone, is controversial. Medulloblastomas, for example, are the most common malignant brain tumour of childhood, but their pathogenesis is unknown, their relationship to other embryonal CNS tumours is debated, and patients' response to therapy is difficult to predict. We approached these problems by developing a classification system based on DNA microarray gene expression data derived from 99 patient samples. Here we demonstrate that medulloblastomas are molecularly distinct from other brain tumours including primitive neuroectodermal tumours (PNETs), atypical teratoid/rhabdoid tumours (AT/RTs) and malignant gliomas. Previously unrecognized evidence supporting the derivation of medulloblastomas from cerebellar granule cells through activation of the Sonic Hedgehog (SHH) pathway was also revealed. We show further that the clinical outcome of children with medulloblastomas is highly predictable on the basis of the gene expression profiles of their tumours at diagnosis. golub-00460 Assay Type: Gene Expression Provider: Affymetrix Array Designs: Hu6800 Organism: Homo sapiens (ncbitax) Material Types: synthetic_RNA, organism_part, whole_organism, total_RNA Disease States: synthetic_RNA, organism_part, whole_orMedulloblastoma, renal rhabdoid tumor, Atypical Teratoid/Rhabdoid Tumor, Supratentorial PNET, Supratentorial PNET (pineoblastoma), Normal, Malignant Glioma, Extrarenal Rhabdoid Tumorganism, total_RNA
2015-05-16 | E-GEOD-68956 | biostudies-arrayexpress
Project description:UHRF1 is an epigenetic regulator that plays critical roles in tumours. However, the DNA methylation alteration patterns driven by UHRF1 and the related differentially expressed tumour-related genes remain unclear. In this study, a UHRF1-shRNA MCF-7 cell line was constructed, and whole-genome bisulfite sequencing (WGBS) and RNA sequencing were performed. The DNA methylation alteration landscape was elucidated, and DNA methylation-altered regions (DMRs) were found to be distributed in both gene bodies and adjacent regions. The DMRs were annotated and categorized into 488 hypermethylated/1696 hypomethylated promoters and 1149 hypermethylated/5501 hypomethylated gene bodies. Through an integrated analysis with the RNA sequencing data, 217 upregulated methylated genes and 288 downregulated methylated genes were identified, and these genes were primarily enriched in nervous system development and cancer signalling pathways.
2024-05-09 | GSE248620 | GEO