← BioTransfer GEO Dataset Finder
GEO series

The transcriptional co-repressor Runx1t1 is essential for N-Myc-driven neuroblastoma tumorigenesis [ChIP-Seq]

GSE230261 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 34 samples Submitted 2024/04/01 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 34 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)
Samples
34 samples: 12 conditions, mostly in triplicateGroups 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
The transcriptional co-repressor Runx1t1 is essential for MYCN-driven neuroblastoma tumorigenesisNature communications · 2024
Summary (written by the submitters)
Changes in epigenetic regulation are believed to be a major contributing factor to neuroblastoma development. Using a large-scale in vivo mutagenesis screen in Th-MYCN transgenic mice, we identified a single point mutation in the transcriptional corepressor Runx1t1, that can block N-Myc-driven neuroblastoma tumorigenesis. The loss of function mutation disrupts a highly conserved zinc finger domain (NHR4) within Runx1t1.
Read the full summary ↓
Crossing an independent Runx1t1 knockout model with Th-MYCN mice, demonstrated that Runx1t1 haploinsufficiency is enough to prevent neuroblastoma development and reverse ganglia hyperplasia. Silencing RUNX1T1 in human neuroblastoma cells resulted in decreased colony formation in vitro, and significant inhibition of tumor growth in vivo. Our results show that RUNX1T1 forms part of a transcriptional LSD1-CoREST3-HDAC repressive complex that regulates the epigenomic landscape and chromatin accessibility, to control neuron-specific pathway genes and maintain an undifferentiated state. Runx1t1 thus represents an entirely novel and highly promising target not previously described in neuroblastoma.
Published in
The transcriptional co-repressor Runx1t1 is essential for MYCN-driven neuroblastoma tumorigenesis
Murray JE, Valli E, Milazzo G et al. · Nature communications 2024 · PMID 38992040 · doi:10.1038/s41467-024-49871-0
This dataset
Open GSE230261 in finder → Find more human ChIP / ATAC / CUT&Tag datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE230261_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA958158 and SRA study SRP433738. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38992040) ↗
Study design
12 conditions, mostly in triplicate
Kelly, H3K27ac, DMSO, ×3 Kelly, H3K27me3, DMSO, ×3 Kelly, H3K4me1, DMSO, ×3 Kelly, H3K4me2, DMSO, ×3 Kelly, H3K4me3, DMSO, ×3 Kelly, H3K27ac, Doxycycline, ×3 Kelly, H3K27me3, Doxycycline, ×3 Kelly, H3K4me1, Doxycycline, ×3 +4 more

Supports a between-group comparison across 34 samples.

How we read this: 12 replicated groups read from 34 sample titles; they account for 34 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.

Samples in this study
Datasets on a similar topic

Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

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.