Generation of a Comprehensive Epigenomic Atlas in Clear Cell Renal Cell Carcinoma Informs Kidney Cancer Progression and Heritability
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 265 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Topic
- Kidney cancerThis series is part of our curated briefing on it.
- Samples
- 265 samples: 251 distinct titles, 11 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Generation of a comprehensive epigenomic atlas in clear cell renal cell carcinoma informs kidney cancer progression and heritabilityCell reports · 2026
Read the full summary ↓
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE309697_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1336758 and SRA study SRP630170. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 265 sample titles: 251 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM9277078 Patient 1077/1284/1308; ATAC-Seq - mets 1
- GSM9277079 Patient 1120; ATAC-Seq - normal
- GSM9277080 Patient 1120; ATAC-Seq - local tumor
- GSM9277081 Patient 1120 (sample no 1124); ATAC-Seq - mets
- GSM9277082 Patient 1247; ATAC-Seq - mets 1
- GSM9277083 Patient 1247; ATAC-Seq - mets 2
- GSM9277084 Patient 1077/1284/1308; ATAC-Seq - mets 2
- GSM9277085 Patient 1077/1284/1308; ATAC-Seq - mets 3
- GSM9277086 Patient 233; ATAC-Seq - normal
- GSM9277087 Patient 233; ATAC-Seq - local tumor
- GSM9277088 Patient 233 (sample no 338); ATAC-Seq - mets
- GSM9277089 Patient 951; ATAC-Seq - normal
- GSM9277090 Patient 951; ATAC-Seq - local tumor
- GSM9277091 Patient 1014; ATAC-Seq - normal
- GSM9277092 Patient 1014; ATAC-Seq - local tumor
- GSM9277093 Patient 1091; ATAC-Seq - normal
- GSM9277094 Patient 1091; ATAC-Seq - local tumor
- GSM9277095 Patient 1091 (sample no 1320); ATAC-Seq - mets
- GSM9277096 Patient 1022; ATAC-Seq - mets
- GSM9277097 Patient 1136; ATAC-Seq - mets
- GSM9277098 Patient 1164; ATAC-Seq - mets
- GSM9277099 Patient 1166; ATAC-Seq - mets
- GSM9277100 Patient 1168; ATAC-Seq - mets
- GSM9277101 Patient 1169; ATAC-Seq - mets
- GSM9277102 Patient 1174; ATAC-Seq - mets
- GSM9277103 Patient 1301; ATAC-Seq - mets
- GSM9277104 Patient 1350; ATAC-Seq - mets
- GSM9277105 Patient 256; ATAC-Seq - mets
- GSM9277106 Patient 344; ATAC-Seq - mets
- GSM9277107 Patient 354; ATAC-Seq - mets
- GSM9277108 Patient 573; ATAC-Seq - mets
- GSM9277109 Patient 964; ATAC-Seq - mets
- GSM9277110 Patient 968; ATAC-Seq - mets
- GSM9277111 Patient 951; ATAC-Seq - mets
- GSM9277112 Patient 962; ATAC-Seq - mets
- GSM9277113 Patient K962; ATAC-Seq - local tumor
- GSM9277114 Patient 957; ATAC-Seq - local tumor
- GSM9277115 Patient 1058; ATAC-Seq - normal
- GSM9277116 Patient 1058; ATAC-Seq - local tumor
- GSM9277117 Patient 957 (sample no 1131); ATAC-Seq - mets
+ 225 more — browse all 265 samples with per-sample file links →
- GSE15641 Gene signatures of progression and metastasis in renal cell cancer 92 samples same disease briefing · shares progression, renal
- GSE216494 Impact of sunitinib resistance on clear cell renal cell carcinoma therapeutic sensitivity in vitro 12 samples same disease briefing · shares clear, renal
- GSE17895 Somatic Mutation Screen of Clear Cell RCC 160 samples same disease briefing · shares clear
- GSE216495 Nonclinical in-vitro evaluation of the transcriptomic and metabolic effects of immune checkpoint inhibitors on sunitinib-resistant renal cell carcinoma 36 samples same disease briefing · shares renal
- GSE19982 Gene expression discriminates chromophobe renal cell carcinoma and oncocytoma 30 samples same disease briefing · shares renal
- GSE174740 Drug repurposing identifies a synergistic high-order drug combination to treat sunitinib-resistant renal cell carcinoma 11 samples same disease briefing · shares renal
- GSE223688 SETD2 loss sensitizes kidney cancer cells to DNA hypomethylating agents 6 samples same disease briefing · shares kidney
- GSE193006 Transcriptome RNA sequencing data of sarcomatoid renal cell carcinoma cell line SRCC and its subclones with different phenotypes. 5 samples same disease briefing · shares renal
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.