Single-cell transcription and chromatin accessbility profiles of IDH mutant gliomas
Single-cell RNA-seq · human · 14 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Topic
- Lower-grade gliomaThis series is part of our curated briefing on it.
- Samples
- 14 samples: 14 samples, each with a distinct title — no replicated groupsGroups 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
- Evolving cell states and oncogenic drivers during the progression of IDH-mutant gliomasNature cancer · 2025
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 GSE241745_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1009671. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 14 sample titles: 14 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.
- GSM7734711 MGH227_scATAC
- GSM7734712 MGH230_scATAC
- GSM7734713 MGH231_scATAC
- GSM7734714 MGH232_scATAC
- GSM7734715 MGH234_scATAC
- GSM7734716 MGH236_scATAC
- GSM7734717 MGH239_scATAC
- GSM7734718 MGH240_scATAC
- GSM7734719 BWH3_scATAC
- GSM7734720 BWH14_scATAC
- GSM7734721 BWH14_primary_scRNA
- GSM7734722 MGH240_primary_scRNA
- GSM7734723 MGH240_organoid_scRNA
- GSM7734724 MGH314_organoid_scRNA
- GSE308634 Transcriptional changes mediated by the HDACi panobinostat in IDH-wildtype and IDH-mutant gliomas 54 samples same disease briefing · shares idh, transcription, gliomas, mutant
- GSE308636 Transcriptional changes mediated by the HDACi belinostat in IDH-mutant glioma cultures with YAP and TAZ overexpression 36 samples same disease briefing · shares idh, transcription, mutant
- GSE70991 Insulator dysfunction and oncogene activation in IDH mutant gliomas 33 samples same disease briefing · shares idh, gliomas, mutant
- GSE252245 Exploiting the therapeutic vulnerability of IDH-mutant gliomas with zotiraciclib 24 samples same disease briefing · shares idh, gliomas, mutant
- GSE134120 Combination of epigenetic enzyme inhibitors, GSKJ4 and Belinostat, reveals efficacy in IDH1 mutant gliomas 16 samples same disease briefing · shares idh, gliomas, mutant
- GSE270109 Single-Cell Sequencing of IDH-Mutant Glioma 4 samples same disease briefing · shares idh, single-cell, mutant
- GSE89567 Single cell RNA-seq analysis of IDH-mutant astrocytoma 6341 samples same disease briefing · shares idh, mutant
- GSE260997 Mutant IDH inhibitors induce lineage differentiation in IDH-mutant Oligodendroglioma III 2458 samples same disease briefing · shares idh, mutant
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.