Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency [CUT&Run]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 169 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)
- Topic
- MedulloblastomaThis series is part of our curated briefing on it.
- Samples
- 169 samples: 57 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.
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 GSE270125_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 PRJNA1125113 and SRA study SRP514481. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 116 samples.
How we read this: 57 replicated groups read from 169 sample titles; they account for 116 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.
- GSM8334856 DMB006_IgG DMB006_IgG
- GSM8334857 Med2312__IgG
- GSM8334858 Rcmb20__IgG
- GSM8334859 Rcmb28__IgG
- GSM8334860 Med1712__IgG
- GSM8334861 Med113__IgG
- GSM8334862 DMB006_H3K27me3
- GSM8334863 Med2312__H3K27me3
- GSM8334864 Rcmb20__H3K27me3
- GSM8334865 Rcmb28__H3K27me3
- GSM8334866 Med1712__H3K27me3
- GSM8334867 Med113__H3K27me3
- GSM8334868 DMB006_H3K4me3 DMB006_H3K4me
- GSM8334869 Med2312__H3K4me3 Med2312__H3K4me
- GSM8334870 Rcmb20__H3K4me3 Rcmb20__H3K4me
- GSM8334871 Rcmb28__H3K4me3 Rcmb28__H3K4me
- GSM8334872 Med1712__H3K4me3 Med1712__H3K4me
- GSM8334873 Med113__H3K4me3 Med113__H3K4me
- GSM8334874 DMB006_H3K4me1 DMB006_H3K4me
- GSM8334875 Med2312__H3K4me1 Med2312__H3K4me
- GSM8334876 Rcmb20__H3K4me1 Rcmb20__H3K4me
- GSM8334877 Rcmb28__H3K4me1 Rcmb28__H3K4me
- GSM8334878 Med1712__H3K4me1 Med1712__H3K4me
- GSM8334879 Med113__H3K4me1 Med113__H3K4me
- GSM8334880 DMB006_EZH2
- GSM8334881 Med2312__EZH2
- GSM8334882 Rcmb20__EZH2
- GSM8334883 Rcmb28__EZH2
- GSM8334884 Med1712__EZH2
- GSM8334885 Med113__EZH2
- GSM8334886 DMB006_KDM2B
- GSM8334887 Med2312__KDM2B
- GSM8334888 Rcmb20__KDM2B
- GSM8334889 Rcmb28__KDM2B
- GSM8334890 Med1712__KDM2B
- GSM8334891 Med113__KDM2B
- GSM8334892 IgG_control_s2 IgG_control_s
- GSM8334893 IgG_control_s3 IgG_control_s
- GSM8334894 KDM2BKO_IgG_s4 KDM2BKO_IgG_s
- GSM8334895 KDM2BKO_IgG_s5 KDM2BKO_IgG_s
+ 129 more — browse all 169 samples with per-sample file links →
- GSE270126 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency. 219 samples same disease briefing · shares kdm2b, medulloblastoma, dependency, divergent, chromatin, selective, disclose
- GSE269909 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency [RNA-Seq] 50 samples same disease briefing · shares kdm2b, medulloblastoma, dependency, divergent, chromatin, selective, disclose
- GSE267470 Dual targeting of processive transcription for Myc-driven circuitry in medulloblastoma [CUT&RUN] 12 samples same disease briefing · shares cut, medulloblastoma
- GSE241602 Dynamic Chromatin Alteration Induces Oncogenic Hijacking by Nuclear Factor I Family Proteins for Medulloblastoma Progression 30 samples same disease briefing · shares medulloblastoma, chromatin
- GSE243558 PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression 29 samples same disease briefing · shares medulloblastoma, chromatin
- GSE37385 Subgroup specific somatic copy number aberrations in the medulloblastoma genome 1382 samples same disease briefing · shares medulloblastoma
- GSE21140 Genomics of medulloblastoma identifies four distinct molecular variants 103 samples same disease briefing · shares medulloblastoma
- GSE243796 Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level 90 samples same disease briefing · shares medulloblastoma
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.