← BioTransfer GEO Dataset Finder
GEO series

Identify H3K4Me3 occupancy on genome in Setd1a Knock out (KO) mouse undifferentiated pleomorphic sarcoma cells

GSE208365 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 10 samples Submitted 2024/05/24 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 10 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
Mus musculus (mouse)
Samples
10 samples: 3 × Metastatic mouse UPS cell, IgG, vs 3 × Metastatic mouse UPS cell lacking Setd1a, IgG, vs 2 × Metastatic mouse UPS cell, H3K4Me3, vs 2 × Metastatic mouse UPS cell lacking Setd1a, H3K4Me3,Groups 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 COMPASS complex maintains the metastatic capacity imparted by a subpopulation of cells in UPSiScience · 2024
Summary (written by the submitters)
As Setd1a is a methyltransferase targeting H3K4, we performed H3K4Me3 ChIP in control and Setd1a KO cell to observe the effects of Setd1a on H3K4Me3. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K4Me in control mouse UPS and Setd1a KO mouse UPS cells .
Published in
The COMPASS complex maintains the metastatic capacity imparted by a subpopulation of cells in UPS
Ban GI, Puviindran V, Xiang Y et al. · iScience 2024 · PMID 38989451 · doi:10.1016/j.isci.2024.110187
This dataset
Open GSE208365 in finder → Find more mouse 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 GSE208365_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 PRJNA859694 and SRA study SRP386861. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38989451) ↗
Study design
3 × Metastatic mouse UPS cell, IgG, vs 3 × Metastatic mouse UPS cell lacking Setd1a, IgG, vs 2 × Metastatic mouse UPS cell, H3K4Me3, vs 2 × Metastatic mouse UPS cell lacking Setd1a, H3K4Me3,

Supports a between-group comparison across 10 samples.

How we read this: 4 replicated groups read from 10 sample titles; they account for 10 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 mouse 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.