Oncogenic fusions converge on shared mechanisms in initiating astroblastoma [RNA-Seq of TREx293]
RNA-seq (gene expression) · human · 10 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
- 10 samples: 5 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
- Oncogenic fusions converge on shared mechanisms in initiating astroblastomaNature · 2025
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 GSE284485_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 PRJNA1199372 and SRA study SRP552126. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 5 replicated groups read from 10 sample titles; they account for 10 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.
- GSM8685083 TREx293_BEND2_rep1 TREx293_BEND2
- GSM8685084 TREx293_BEND2_rep2 TREx293_BEND2
- GSM8685085 TREx293_CTRL_rep1 TREx293_CTRL
- GSM8685086 TREx293_CTRL_rep2 TREx293_CTRL
- GSM8685087 TREx293_MN1_rep1 TREx293_MN1
- GSM8685088 TREx293_MN1_rep2 TREx293_MN1
- GSM8685089 TREx293_MN1-BEND2_rep1 TREx293_MN1-BEND2
- GSM8685090 TREx293_MN1-BEND2_rep2 TREx293_MN1-BEND2
- GSM8685091 TREx293_MN1-CXXC5_rep1 TREx293_MN1-CXXC5
- GSM8685092 TREx293_MN1-CXXC5_rep2 TREx293_MN1-CXXC5
- GSE267717 Gain-of-function RNA Polymerase II partitioning is a shared feature of diverse oncogenic fusions 14 samples shares oncogenic, fusions, shared
- GSE229541 Amplified dosage of the NKX2-1 lineage transcription factor controls its oncogenic role in lung adenocarcinoma [RNA-seq] 102 samples shares oncogenic, rna-seq
- GSE296212 LINE-1 locus transcription nucleates oncogenic chromatin architecture [RNA-Seq] 80 samples shares oncogenic, rna-seq
- GSE293331 Allelic topological centering by transcription factors drives oncogenic multi-enhancer transcriptional regulation [RNA-seq] 54 samples shares oncogenic, rna-seq
- GSE211354 The SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma [RNA-Seq] 54 samples shares oncogenic, rna-seq
- GSE275705 Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription [RNA-seq II] 36 samples shares oncogenic, rna-seq
- GSE293856 Alphavirus M1 disrupts super-enhancer-driven oncogenic transcription in osteosarcoma [RNA-seq] 32 samples shares oncogenic, rna-seq
- GSE279872 Targeting FOXA1 and FOXA2 Disrupts the Lineage-Specific Oncogenic Output in Prostate Cancer [RNA-seq] 30 samples shares oncogenic, 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.