Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency.
RNA-seq (gene expression) · human · 219 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)
- Topic
- MedulloblastomaThis series is part of our curated briefing on it.
- Samples
- 219 samples: 65 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.
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 GSE270126_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 PRJNA1125058 and SRA study SRP514105. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 139 samples.
How we read this: 65 replicated groups read from 219 sample titles; they account for 139 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.
- GSM8330111 D283_Day4_control_rep1 D283_Day4_control
- GSM8330112 D283_Day4_control_rep2 D283_Day4_control
- GSM8330113 D283_Day4_control_rep3 D283_Day4_control
- GSM8330114 D283_Day4_KDM2B_gRNA10_rep1 D283_Day4_KDM2B_gRNA10
- GSM8330115 D283_Day4_KDM2B_gRNA10_rep2 D283_Day4_KDM2B_gRNA10
- GSM8330116 D283_Day4_KDM2B_gRNA10_rep3 D283_Day4_KDM2B_gRNA10
- GSM8330117 D283_Day4_KDM2B_gRNA28_rep1 D283_Day4_KDM2B_gRNA28
- GSM8330118 D283_Day4_KDM2B_gRNA28_rep2 D283_Day4_KDM2B_gRNA28
- GSM8330119 D283_Day4_KDM2B_gRNA28_rep3 D283_Day4_KDM2B_gRNA28
- GSM8330120 D283_Day7_control_rep1 D283_Day7_control
- GSM8330121 D283_Day7_control_rep2 D283_Day7_control
- GSM8330122 D283_Day7_control_rep3 D283_Day7_control
- GSM8330123 D283_Day7_KDM2B_gRNA10_rep1 D283_Day7_KDM2B_gRNA10
- GSM8330124 D283_Day7_KDM2B_gRNA10_rep2 D283_Day7_KDM2B_gRNA10
- GSM8330125 D283_Day7_KDM2B_gRNA10_rep3 D283_Day7_KDM2B_gRNA10
- GSM8330126 D283_Day7_KDM2B_gRNA28_rep1 D283_Day7_KDM2B_gRNA28
- GSM8330127 D283_Day7_KDM2B_gRNA28_rep2 D283_Day7_KDM2B_gRNA28
- GSM8330128 D283_Day7_KDM2B_gRNA28_rep3 D283_Day7_KDM2B_gRNA28
- GSM8330129 DMB006_control_rep1 DMB006_control
- GSM8330130 DMB006_control_rep2 DMB006_control
- GSM8330131 DMB006_gRNA10_rep1 DMB006_gRNA10
- GSM8330132 DMB006_gRNA10_rep2 DMB006_gRNA10
- GSM8330133 DMB006_gRNA10_rep3 DMB006_gRNA10
- GSM8330134 DMB006_control_rep1_batch2
- GSM8330135 DMB006_control_rep2_batch2
- GSM8330136 DMB006_control_rep3_batch2
- GSM8330137 DMB006_gRNA10_rep1_batch2
- GSM8330138 DMB006_gRNA10_rep2_batch2
- GSM8330139 DMB006_gRNA10_rep3_batch2
- GSM8330140 DMB006_gRNA28_rep1_batch2
- GSM8330141 DMB006_gRNA28_rep2_batch2
- GSM8330142 DMB006_gRNA28_rep3_batch2
- 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
+ 179 more — browse all 219 samples with per-sample file links →
- GSE270125 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency [CUT&Run] 169 samples same disease briefing · shares kdm2b, medulloblastoma, dependency, divergent, chromatin, selective, disclose, states
- 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, states
- 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
- GSE254917 Sonic hedgehog medulloblastoma cells in co-culture with cerebellar organoids converge towards in vivo malignant cell states 7 samples same disease briefing · shares medulloblastoma, states
- 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.