Metabolic reprogramming driven by TFE3 fusions unveils novel vulnerabilities in translocation renal cell carcinoma [RNA-Seq]
RNA-seq (gene expression) · human · 24 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 24 samples: 8 conditions, mostly in triplicateGroups 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 GSE266517_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1107488 and SRA study SRP505949. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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.
- GSM8248728 sTFE_Ctrl_sgRNA_rep1 sTFE_Ctrl_sgRNA
- GSM8248729 sTFE_Ctrl_sgRNA_rep2 sTFE_Ctrl_sgRNA
- GSM8248730 sTFE_Ctrl_sgRNA_rep3 sTFE_Ctrl_sgRNA
- GSM8248731 sTFE_TFE3KD_rep1 sTFE_TFE3KD
- GSM8248732 sTFE_TFE3KD_rep2 sTFE_TFE3KD
- GSM8248733 sTFE_TFE3KD_rep3 sTFE_TFE3KD
- GSM8248734 786-O_TFE3KD_nodox_rep1 786-O_TFE3KD_nodox
- GSM8248735 786-O_TFE3KD_nodox_rep2 786-O_TFE3KD_nodox
- GSM8248736 786-O_TFE3KD_nodox_rep3 786-O_TFE3KD_nodox
- GSM8248737 786-O_TFE3KD_dox_rep1 786-O_TFE3KD_dox
- GSM8248738 786-O_TFE3KD_dox_rep2 786-O_TFE3KD_dox
- GSM8248739 786-O_TFE3KD_dox_rep3 786-O_TFE3KD_dox
- GSM8248740 UOK109_rep1 UOK109
- GSM8248741 UOK109_rep2 UOK109
- GSM8248742 UOK109_rep3 UOK109
- GSM8248743 UOK146_rep1 UOK146
- GSM8248744 UOK146_rep2 UOK146
- GSM8248745 UOK146_rep3 UOK146
- GSM8248746 FU-UR-1_TFE3KD_nodox_rep1 FU-UR-1_TFE3KD_nodox
- GSM8248747 FU-UR-1_TFE3KD_nodox_rep2 FU-UR-1_TFE3KD_nodox
- GSM8248748 FU-UR-1_TFE3KD_nodox_rep3 FU-UR-1_TFE3KD_nodox
- GSM8248749 FU-UR-1_TFE3KD_dox_rep1 FU-UR-1_TFE3KD_dox
- GSM8248750 FU-UR-1_TFE3KD_dox_rep2 FU-UR-1_TFE3KD_dox
- GSM8248751 FU-UR-1_TFE3KD_dox_rep3 FU-UR-1_TFE3KD_dox
- GSE268092 TFE3 fusion proteins drive oxidative metabolism, ferroptosis resistance and general RNA synthesis in translocation renal cell carcinoma. [RNA-seq] 36 samples shares tfe3, translocation, rna-seq
- GSE235738 Alveolar Soft Part Sarcoma is driven by ASPSCR1::TFE3-dependent and therapeutically targetable transcriptional programs [RNA-Seq] 35 samples shares tfe3, rna-seq, driven
- GSE328026 MiT Fusions, TSC1–TSC2 Divergence, and Stem-like Programs Reveal Distinct Origins and Vulnerabilities in PEComa [RNA-seq] 69 samples shares vulnerabilities, fusions, rna-seq
- GSE281165 TFE3 fusion oncoprotein condensates drive epigenetic reprogramming and cancer progression [CUT&RUN] 43 samples shares tfe3, reprogramming
- GSE294016 A macrophage-predominant, immunosuppressive immune microenvironment and subtype-specific therapeutic vulnerabilities in advanced salivary gland cancer [bulk RNA-seq] 95 samples shares vulnerabilities, rna-seq
- GSE232076 In vitro reconstitution of epigenetic reprogramming in the human germ line [RNA-Seq] 89 samples shares reprogramming, rna-seq
- GSE298209 Chemical reprogramming of human blood cells into hCiPS cells [bulk RNA-seq] 62 samples shares reprogramming, rna-seq
- GSE324642 Canonical and isomiR products of miR-142 enhance dendritic cell reprogramming [bulk RNA-seq] 53 samples shares reprogramming, rna-seq
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.