Single-nuclei ATAC-Seq profiles from Group 3 and Group 4 medulloblastomas [scATAC-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 33 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)
- Samples
- 33 samples: 33 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 GSE253573_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 PRJNA1066320. 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 33 sample titles: 33 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.
- GSM8023709 MB278_10xATAC
- GSM8023710 MB89_10xATAC
- GSM8023711 MB183_10xATAC
- GSM8023712 MB26_10xATAC
- GSM8023713 MB297_10xATAC
- GSM8023714 MB99_10xATAC
- GSM8023715 MB279_10xATAC
- GSM8023716 MB5_10xATAC
- GSM8023717 MB18_10xATAC
- GSM8023718 MB165_10xATAC
- GSM8023719 MB166_10xATAC
- GSM8023720 MB177_10xATAC
- GSM8023721 MB38_10xATAC
- GSM8023722 MB86_10xATAC
- GSM8023723 MB90_10xATAC
- GSM8023724 MB134_10xATAC
- GSM8023725 MB249_10xATAC
- GSM8023726 MB96_10xATAC
- GSM8023727 MB98_10xATAC
- GSM8023728 MB164_10xATAC
- GSM8023729 MB272_10xATAC
- GSM8023730 MB110_10xATAC
- GSM8023731 MB294_10xATAC
- GSM8023732 MB129_10xATAC
- GSM8023733 INF_R_447_10xATAC
- GSM8023734 MB292_10xATAC
- GSM8023735 N4059_22_10xATAC
- GSM8023736 INF_R_46_10xATAC
- GSM8023737 INF_R_1237_10xATAC
- GSM8023738 MB272_R_10xATAC
- GSM8023739 INF_P_637_10xATAC
- GSM8023740 INF_R_637_10xATAC
- GSM8023741 MB248_10xATAC
- GSE253557 Single-nuclei RNA-Seq profiles from Group 3 and Group 4 medulloblastomas [scRNA-Seq] 39 samples shares medulloblastomas, single-nuclei, profiles, group
- GSE270684 The EZH2 and EZH1 inhibitor valemetostat derepresses p16INK4a to induce early endomitotic exit in megakaryocytes [scATAC-Seq] 66 samples shares scatac-seq, atac-seq
- GSE281809 Enhancing single-cell ATAC sequencing with formaldehyde fixation, cryopreservation, and multiplexing for flexible analysis [scATAC-seq] 10 samples shares scatac-seq, atac-seq
- GSE301714 Mezigdomide reverses T cell exhaustion through degradation of Aiolos/Ikaros and reinvigoration of cytokine production pathways [scATAC-seq] 8 samples shares scatac-seq, atac-seq
- GSE93646 Microarray-based DNA methylation profiles of primary medulloblastomas 428 samples shares medulloblastomas, profiles
- GSE281526 Single-nuclei RNA-seq and ATAC-seq for Human Retina from Diverse Ancestry Backgrounds 185 samples shares single-nuclei, atac-seq
- GSE278880 Isocitrate Dehydrogenase 1 Primes Group-3 Medulloblastomas For Cuproptosis 36 samples shares medulloblastomas, group
- GSE278751 A stem cell model identifies two alternative cell fates in CBFA2T3::GLIS2-driven acute megakaryoblastic leukemia initiation (Multiome scRNA-seq/scATAC-seq) 14 samples shares scatac-seq, atac-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.