5-hydroxymethylcytosine deposition mediates Polycomb Repressive Complex 2 function in MYCN-amplified neuroblastoma [CUT&Run]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 18 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
- NeuroblastomaThis series is part of our curated briefing on it.
- Samples
- 18 samples: 16 distinct titles, 2 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 GSE294307_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 PRJNA1248984 and SRA study SRP577985. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 18 sample titles: 16 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.
- GSM8902167 BE2 WT, IgG, EpiCypher, rep 1
- GSM8902168 BE2 TET2KO 1, IgG, EpiCypher, rep 1
- GSM8902169 BE2 TET2KO 2, IgG, EpiCypher, rep 1
- GSM8902170 BE2 TET2KO 3, IgG, EpiCypher, rep 1
- GSM8902171 BE2 WT, H3K27me3, CST, rep 1
- GSM8902172 BE2 TET2KO 1, H3K27me3, CST, rep 1
- GSM8902173 BE2 TET2KO 2, H3K27me3, CST, rep 1
- GSM8902174 BE2 TET2KO 3, H3K27me3, CST, rep 1
- GSM8902175 BE2 H2O, IgG, EpiCypher, rep 1
- GSM8902176 BE2 CoCl2 10, IgG, EpiCypher, rep 1
- GSM8902177 BE2 CoCl2 50, IgG, EpiCypher, rep 1
- GSM8902178 BE2 H2O, H3K27me3, CST, rep 1
- GSM8902179 BE2 CoCl2 10, H3K27me3, CST, rep 1
- GSM8902180 BE2 CoCl2 50, H3K27me3, CST, rep 1
- GSM8902181 BE2 WT, H3K27me3, CST, rep 2
- GSM8902182 WN WT, H3K27me3, CST, rep 2
- GSM8902183 BE2 WT, IgG, EpiCypher, rep 2
- GSM8902184 WN WT, IgG, EpiCypher, rep 2
- GSE164456 Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma 69 samples same disease briefing · shares mycn-amplified, neuroblastoma
- GSE112914 Differential gene expression analysis of MYCN-amplified neuroblastoma cells after Doxycycline inducible shRNA knockdown of JMJD6 gene expression 44 samples same disease briefing · shares mycn-amplified, neuroblastoma
- GSE120572 A mechanistic classification of clinical phenotypes in neuroblastoma 394 samples same disease briefing · shares neuroblastoma
- GSE181582 IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression 264 samples same disease briefing · shares neuroblastoma
- GSE12494 SNP data from Neuroblastoma samples 262 samples same disease briefing · shares neuroblastoma
- GSE16476 Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma 88 samples same disease briefing · shares neuroblastoma
- GSE130612 Multi-omics analysis of neuroblastoma cells reveals a diversity of malignant transformations 64 samples same disease briefing · shares neuroblastoma
- GSE153823 Effect of ASCL1 phosphorylation status on chromatin binding and target regulation in neuroblastoma 52 samples same disease briefing · shares neuroblastoma
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.