Isocitrate Dehydrogenase 1 Primes Group-3 Medulloblastomas For Cuproptosis
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 36 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
- 36 samples: 28 distinct titles, 4 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.
- Paper
- Isocitrate dehydrogenase 1 primes group-3 medulloblastomas for cuproptosisCancer cell · 2025
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 GSE278880_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 PRJNA1169346 and SRA study SRP536794. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 36 sample titles: 28 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.
- GSM8556546 D283_Parental_DMSO_1
- GSM8556547 D283_Parental_DMSO_2
- GSM8556548 D283_Parental_DMSO_3
- GSM8556549 D283_Elesclomol_1
- GSM8556550 D283_Elesclomol_2
- GSM8556551 D283_Elesclomol_3
- GSM8556552 CB_SV40_1
- GSM8556553 CB_SV40_2
- GSM8556554 CB_SV40_3
- GSM8556555 CB_MYC_1
- GSM8556556 CB_MYC_2
- GSM8556557 CB_MYC_3
- GSM8574409 D283_cells_1 (ATAC-seq)
- GSM8574410 D283_cells_2 (ATAC-seq)
- GSM8574411 D283_cells_3 (ATAC-seq)
- GSM8574412 D283_cells_IDH1_siRNA_1 (ATAC-seq)
- GSM8574413 D283_cells_IDH1_siRNA_2 (ATAC-seq)
- GSM8574414 D283_cells_IDH1_siRNA_3 (ATAC-seq)
- GSM8574415 D283_ctrl_k4me3_1 (CUT&RUN)
- GSM8574416 D283_ctrl_k4me3_2 (CUT&RUN)
- GSM8574417 D283_ctrl_k4me3_3 (CUT&RUN)
- GSM8574418 D283_treat_k4me3_1 (CUT&RUN)
- GSM8574419 D283_treat_k4me3_2 (CUT&RUN)
- GSM8574420 D283_treat_k4me3_3 (CUT&RUN)
- GSM8574421 D283_ctrl_k27me3_1 (CUT&RUN)
- GSM8574422 D283_ctrl_k27me3_2 (CUT&RUN)
- GSM8574423 D283_ctrl_k27me3_3 (CUT&RUN)
- GSM8574424 D283_treat_k27me3_1 (CUT&RUN)
- GSM8574425 D283_treat_k27me3_2 (CUT&RUN)
- GSM8574426 D283_treat_k27me3_3 (CUT&RUN)
- GSM8574427 D283_ctrl_k9me3_1 (CUT&RUN)
- GSM8574428 D283_ctrl_k9me3_2 (CUT&RUN)
- GSM8574429 D283_ctrl_k9me3_3 (CUT&RUN)
- GSM8574430 D283_treat_k9me3_1 (CUT&RUN)
- GSM8574431 D283_treat_k9me3_2 (CUT&RUN)
- GSM8574432 D283_treat_k9me3_3 (CUT&RUN)
- GSE253557 Single-nuclei RNA-Seq profiles from Group 3 and Group 4 medulloblastomas [scRNA-Seq] 39 samples same disease briefing · shares medulloblastomas
- GSE226733 Effect of knockdown of Musashi-1 in Group 3/4 medulloblastomas cells 6 samples same disease briefing · shares medulloblastomas
- GSE283621 Single-cell multi-omics analysis identifies metabolism-linked epigenetic reprogramming as a driver of therapy-resistant medulloblastoma 79 samples same disease briefing
- GSE217639 Effect of ZIC1 on group 3 medulloblastoma cell lines and granule neuron progenitor 49 samples same disease briefing
- GSE243558 PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression 29 samples same disease briefing
- GSE37385 Subgroup specific somatic copy number aberrations in the medulloblastoma genome 1382 samples same disease briefing
- GSE270126 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency. 219 samples same disease briefing
- GSE270125 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency [CUT&Run] 169 samples same disease briefing
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.