Single-nuclei RNA-Seq profiles from Group 3 and Group 4 medulloblastomas [scRNA-Seq]
Single-nucleus RNA-seq · human · 39 samples
- What it is
- Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
- Organism
- Homo sapiens (human)
- Topic
- MedulloblastomaThis series is part of our curated briefing on it.
- Samples
- 39 samples: 39 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
- Oncogene aberrations drive medulloblastoma progression, not initiationNature · 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 GSE253557_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 PRJNA1066283. 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 39 sample titles: 39 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.
- GSM8023165 Combined_10xRNA
- GSM8023166 MB278_10xRNA
- GSM8023167 MB18_10xRNA
- GSM8023168 MB248_10xRNA
- GSM8023169 MB272_10xRNA
- GSM8023170 MB296_10xRNA
- GSM8023171 MB96_10xRNA
- GSM8023172 MB98_10xRNA
- GSM8023173 MB164_10xRNA
- GSM8023174 MB5_10xRNA
- GSM8023175 MB90_10xRNA
- GSM8023176 MB166_10xRNA
- GSM8023177 MB89_10xRNA
- GSM8023178 MB134_10xRNA
- GSM8023179 MB165_10xRNA
- GSM8023180 MB294_10xRNA
- GSM8023181 MB177_10xRNA
- GSM8023182 MB38_10xRNA
- GSM8023183 MB86_10xRNA
- GSM8023184 MB2033_10xRNA
- GSM8023185 MB91_10xRNA
- GSM8023186 MB110_10xRNA
- GSM8023187 MB26_10xRNA
- GSM8023188 MB183_10xRNA
- GSM8023189 MB297_10xRNA
- GSM8023190 MB99_10xRNA
- GSM8023191 MB129_10xRNA
- GSM8023192 MB249_10xRNA
- GSM8023193 MB279_10xRNA
- GSM8023194 MB1935_10xRNA
- GSM8023195 MB1947_10xRNA
- GSM8023196 INF_R_44_10xRNA
- GSM8023197 MB292_10xRNA
- GSM8023198 N4059_22_10xRNA
- GSM8023199 INF_R_46_10xRNA
- GSM8023200 INF_R_12_10xRNA
- GSM8023201 MB272_R_10xRNA
- GSM8023202 INF_P_63_10xRNA
- GSM8023203 INF_R_63_10xRNA
- GSE263652 Human cerebellar organoids to study medulloblastoma pathogenesis and treatment. [scRNA-Seq] 17 samples same disease briefing · shares scrna-seq, rna-seq
- GSE226733 Effect of knockdown of Musashi-1 in Group 3/4 medulloblastomas cells 6 samples same disease briefing · shares medulloblastomas, group
- GSE288463 AMBRA1 as a novel positive regulator of the SHH pathway in medulloblastoma [scRNA-seq] 2 samples same disease briefing · shares scrna-seq, rna-seq
- GSE278880 Isocitrate Dehydrogenase 1 Primes Group-3 Medulloblastomas For Cuproptosis 36 samples same disease briefing · shares medulloblastomas, group
- GSE269909 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency [RNA-Seq] 50 samples same disease briefing · shares rna-seq
- GSE323995 CReP-mediated control of eIF2a phosphorylation is a central node in high-risk medulloblastoma [RNA-Seq 3] 48 samples same disease briefing · shares rna-seq
- GSE206899 Prtg+ve Rhombic Lip Ventricular Zone Stem Cells Initiate and Maintain Group 3 Medulloblastoma. 24 samples same disease briefing · shares group
- GSE267469 Dual targeting of processive transcription for Myc-driven circuitry in medulloblastoma [RNA-seq] 24 samples same disease briefing · shares 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.