PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 29 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
- 29 samples: 9 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.
- Paper
- PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expressionScientific reports · 2024
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 GSE243558_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 PRJNA1018917 and SRA study SRP461673. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 29 samples.
How we read this: 9 replicated groups read from 29 sample titles; they account for 29 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.
- GSM7790883 NES, EV, Replicate 1 NES, EV,
- GSM7790884 NES, EV, Replicate 2 NES, EV,
- GSM7790885 NES, EV, Replicate 3 NES, EV,
- GSM7790886 NES, PRDM6, Replicate 1 NES, PRDM6,
- GSM7790887 NES, PRDM6, Replicate 2 NES, PRDM6,
- GSM7790888 NES, PRDM6, Replicate 3 NES, PRDM6,
- GSM7790889 PRDM6 NES-derived tumor, 94957 PRDM6 NES-derived tumor,
- GSM7790890 PRDM6 NES-derived tumor, 94958 PRDM6 NES-derived tumor,
- GSM7790891 PRDM6 NES-derived tumor, 94856 PRDM6 NES-derived tumor,
- GSM7790892 MYCN NES-derived tumor, 94861 MYCN NES-derived tumor,
- GSM7790893 MYCN NES-derived tumor, 94863 MYCN NES-derived tumor,
- GSM7790894 MYCN NES-derived tumor, 94973 MYCN NES-derived tumor,
- GSM7790895 PRDM6-MYCN NES-derived tumor, 94836 PRDM6-MYCN NES-derived …
- GSM7790896 PRDM6-MYCN NES-derived tumor, 94840 PRDM6-MYCN NES-derived …
- GSM7790897 PRDM6-MYCN NES-derived tumor, 94867 PRDM6-MYCN NES-derived …
- GSM7790922 NES, EV, Replicate 1 NES, EV,
- GSM7790923 NES, EV, Replicate 2 NES, EV,
- GSM7790924 NES, EV, Replicate 3 NES, EV,
- GSM7790925 NES, PRDM6, Replicate 1 NES, PRDM6,
- GSM7790926 NES, PRDM6, Replicate 2 NES, PRDM6,
- GSM7790927 NES, PRDM6, Replicate 3 NES, PRDM6,
- GSM7790928 NES, PRDM6, H3K27me3 CUT&RUN, Replicate 1 NES, PRDM6, H3K27me3 CU…
- GSM7790929 NES, PRDM6, H3K27me3 CUT&RUN, Replicate 2 NES, PRDM6, H3K27me3 CU…
- GSM7790930 NES, EV, V5 CUT&RUN, Replicate 1 NES, EV, V5 CUT&RUN,
- GSM7790931 NES, EV, V5 CUT&RUN, Replicate 2 NES, EV, V5 CUT&RUN,
- GSM7790932 NES, PRDM6, V5 CUT&RUN, Replicate 1 NES, PRDM6, V5 CUT&RUN,
- GSM7790933 NES, PRDM6, V5 CUT&RUN, Replicate 2 NES, PRDM6, V5 CUT&RUN,
- GSM8273686 NES, EV, H3K27me3 CUT&RUN, Replicate 1 NES, EV, H3K27me3 CUT&R…
- GSM8273687 NES, EV, H3K27me3 CUT&RUN, Replicate 2 NES, EV, H3K27me3 CUT&R…
- GSE270126 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency. 219 samples same disease briefing · shares medulloblastoma, chromatin
- GSE270125 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency [CUT&Run] 169 samples same disease briefing · shares medulloblastoma, chromatin
- GSE269909 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency [RNA-Seq] 50 samples same disease briefing · shares medulloblastoma, chromatin
- GSE241602 Dynamic Chromatin Alteration Induces Oncogenic Hijacking by Nuclear Factor I Family Proteins for Medulloblastoma Progression 30 samples same disease briefing · shares medulloblastoma, chromatin
- GSE283621 Single-cell multi-omics analysis identifies metabolism-linked epigenetic reprogramming as a driver of therapy-resistant medulloblastoma 79 samples same disease briefing · shares medulloblastoma
- GSE217639 Effect of ZIC1 on group 3 medulloblastoma cell lines and granule neuron progenitor 49 samples same disease briefing · shares medulloblastoma
- GSE278880 Isocitrate Dehydrogenase 1 Primes Group-3 Medulloblastomas For Cuproptosis 36 samples same disease briefing · shares medulloblastoma
- GSE37385 Subgroup specific somatic copy number aberrations in the medulloblastoma genome 1382 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.