Metabolic reprogramming driven by TFE3 fusions unveils novel vulnerabilities in translocation renal cell carcinoma [ChIP-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 32 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
- 32 samples: 16 conditions, mostly in duplicateGroups 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
- TFE3 fusions direct an oncogenic transcriptional program that drives OXPHOS and unveils vulnerabilities in translocation renal cell carcinomabioRxiv : the preprint server for biology · 2024
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 GSE266530_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 PRJNA1107519 and SRA study SRP505617. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 32 samples.
How we read this: 16 replicated groups read from 32 sample titles; they account for 32 of them. 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.
- GSM8249257 786-O H3K27ac input_rep1 786-O H3K27ac input
- GSM8249258 786-O H3K27ac input_rep2 786-O H3K27ac input
- GSM8249259 786-O H3K27ac ChIP_rep1 786-O H3K27ac ChIP
- GSM8249260 786-O H3K27ac ChIP_rep2 786-O H3K27ac ChIP
- GSM8249261 UOK109 H3K27ac input_rep1 UOK109 H3K27ac input
- GSM8249262 UOK109 H3K27ac input_rep2 UOK109 H3K27ac input
- GSM8249263 UOK109 H3K27ac ChIP_rep1 UOK109 H3K27ac ChIP
- GSM8249264 UOK109 H3K27ac ChIP_rep2 UOK109 H3K27ac ChIP
- GSM8249265 UOK146 H3K27ac input_rep1 UOK146 H3K27ac input
- GSM8249266 UOK146 H3K27ac input_rep2 UOK146 H3K27ac input
- GSM8249267 UOK146 H3K27ac ChIP_rep1 UOK146 H3K27ac ChIP
- GSM8249268 UOK146 H3K27ac ChIP_rep2 UOK146 H3K27ac ChIP
- GSM8249269 FU-UR-1 H3K27 ChIP rep1 FU-UR-1 H3K27 ChIP
- GSM8249270 FU-UR-1 H3K27 ChIP rep2 FU-UR-1 H3K27 ChIP
- GSM8249271 FU-UR-1 H3K27 Input rep1 FU-UR-1 H3K27 Input
- GSM8249272 FU-UR-1 H3K27 Input rep2 FU-UR-1 H3K27 Input
- GSM8249273 s-TFE H3K27ac input_rep1 s-TFE H3K27ac input
- GSM8249274 s-TFE H3K27ac input_rep2 s-TFE H3K27ac input
- GSM8249275 s-TFE H3K27ac ChIP_rep1 s-TFE H3K27ac ChIP
- GSM8249276 s-TFE H3K27ac ChIP_rep2 s-TFE H3K27ac ChIP
- GSM8249277 UOK109 TFE3 input_rep1 UOK109 TFE3 input
- GSM8249278 UOK109 TFE3 input_rep2 UOK109 TFE3 input
- GSM8249279 UOK109 TFE3 ChIP_rep1 UOK109 TFE3 ChIP
- GSM8249280 UOK109 TFE3 ChIP_rep2 UOK109 TFE3 ChIP
- GSM8249281 FU-UR-1 TFE3 input_rep1 FU-UR-1 TFE3 input
- GSM8249282 FU-UR-1 TFE3 input_rep2 FU-UR-1 TFE3 input
- GSM8249283 FU-UR-1 TFE3 ChIP_rep1 FU-UR-1 TFE3 ChIP
- GSM8249284 FU-UR-1 TFE3 ChIP_rep2 FU-UR-1 TFE3 ChIP
- GSM8249285 s-TFE TFE3 input_rep1 s-TFE TFE3 input
- GSM8249286 s-TFE TFE3 input_rep2 s-TFE TFE3 input
- GSM8249287 s-TFE TFE3 ChIP_rep1 s-TFE TFE3 ChIP
- GSM8249288 s-TFE TFE3 ChIP_rep2 s-TFE TFE3 ChIP
- GSE17895 Somatic Mutation Screen of Clear Cell RCC 160 samples same disease briefing
- GSE15641 Gene signatures of progression and metastasis in renal cell cancer 92 samples same disease briefing
- GSE22316 PBRM1 Knockdown in RCC Cell Lines 89 samples same disease briefing
- 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
- GSE19982 Gene expression discriminates chromophobe renal cell carcinoma and oncocytoma 30 samples same disease briefing
- GSE214635 The E3 ligase RBCK1 reduces the sensitivity of ccRCC to sunitinib through the ANKRD35-MITD1-ANXA1 axis 18 samples same disease briefing
- GSE216494 Impact of sunitinib resistance on clear cell renal cell carcinoma therapeutic sensitivity in vitro 12 samples same disease briefing
- GSE174740 Drug repurposing identifies a synergistic high-order drug combination to treat sunitinib-resistant renal cell carcinoma 11 samples same disease briefing
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.