Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency [RNA-Seq]
RNA-seq (gene expression) · human · 50 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
- 50 samples: 35 distinct titles, 8 of them repeatedGroups 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 GSE269909_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 PRJNA1124104 and SRA study SRP514105. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 50 sample titles: 35 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.
- GSM8330111 D283_Day4_control_rep1
- GSM8330112 D283_Day4_control_rep2
- GSM8330113 D283_Day4_control_rep3
- GSM8330114 D283_Day4_KDM2B_gRNA10_rep1
- GSM8330115 D283_Day4_KDM2B_gRNA10_rep2
- GSM8330116 D283_Day4_KDM2B_gRNA10_rep3
- GSM8330117 D283_Day4_KDM2B_gRNA28_rep1
- GSM8330118 D283_Day4_KDM2B_gRNA28_rep2
- GSM8330119 D283_Day4_KDM2B_gRNA28_rep3
- GSM8330120 D283_Day7_control_rep1
- GSM8330121 D283_Day7_control_rep2
- GSM8330122 D283_Day7_control_rep3
- GSM8330123 D283_Day7_KDM2B_gRNA10_rep1
- GSM8330124 D283_Day7_KDM2B_gRNA10_rep2
- GSM8330125 D283_Day7_KDM2B_gRNA10_rep3
- GSM8330126 D283_Day7_KDM2B_gRNA28_rep1
- GSM8330127 D283_Day7_KDM2B_gRNA28_rep2
- GSM8330128 D283_Day7_KDM2B_gRNA28_rep3
- GSM8330129 DMB006_control_rep1
- GSM8330130 DMB006_control_rep2
- GSM8330131 DMB006_gRNA10_rep1
- GSM8330132 DMB006_gRNA10_rep2
- GSM8330133 DMB006_gRNA10_rep3
- 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
- GSM9570159 3358458_D283_Ctrl_Rep1
- GSM9570160 3358459_D283_KDM2B_degradation_Rep1
- GSM9570161 3358460_D283_KDM2B_degradation_rescued_by_KDM2B_Rep1
- GSM9570162 3358461_D283_KDM2B_degradation_rescued_by_KDM2B_CXXC_deletion_Rep1
- GSM9570163 3358462_D283_KDM2B_degradation_rescued_by_KDM2B_JmjC_deletion_Rep1
- GSM9570164 3358463_D283_KDM2B_degradation_rescued_by_KDM2B_JmjC_mutation_Rep1
- GSM9570165 3358464_D283_Ctrl_Rep2
- GSM9570166 3358465_D283_KDM2B_degradation_Rep2
+ 10 more — browse all 50 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
- 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
- GSE323995 CReP-mediated control of eIF2a phosphorylation is a central node in high-risk medulloblastoma [RNA-Seq 3] 48 samples same disease briefing · shares medulloblastoma, rna-seq
- GSE253557 Single-nuclei RNA-Seq profiles from Group 3 and Group 4 medulloblastomas [scRNA-Seq] 39 samples same disease briefing · shares medulloblastoma, rna-seq
- GSE241602 Dynamic Chromatin Alteration Induces Oncogenic Hijacking by Nuclear Factor I Family Proteins for Medulloblastoma Progression 30 samples same disease briefing · shares medulloblastoma, chromatin
- GSE267469 Dual targeting of processive transcription for Myc-driven circuitry in medulloblastoma [RNA-seq] 24 samples same disease briefing · shares medulloblastoma, rna-seq
- GSE243795 Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level [RNA-Seq] 21 samples same disease briefing · shares medulloblastoma, rna-seq
- GSE230865 PolyA RNA-seq from Medulloblastoma cells ± EYA2 knockdown 18 samples same disease briefing · shares medulloblastoma, 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.