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PROSER1 Modulates DNA Demethylation through Dual Mechanisms to Prevent Syndromic Developmental Malformations

GSE273517 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 41 samples Submitted 2024/11/20 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 41 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
41 samples: 17 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
PROSER1 modulates DNA demethylation through dual mechanisms to prevent syndromic developmental malformationsGenes & development · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
PROSER1 modulates DNA demethylation through dual mechanisms to prevent syndromic developmental malformations
Fleming A, Knatko EV, Li X et al. · Genes & development 2024 · PMID 39562138 · doi:10.1101/gad.352176.124
This dataset
Open GSE273517 in finder → Find more mouse RNA-seq 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 GSE273517_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 PRJNA1142037 and SRA study SRP523433. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39562138) ↗
Study design
17 conditions, mostly in duplicate
wildtype mESC H3K27ac ChIP biol ×3 PROSER1 knockout mESC H3K27ac ChIP biol ×3 wildtype mESC H3K4me1 ChIP biol ×3 PROSER1 knockout mESC H3K4me1 ChIP biol ×3 wildtype mESC TET2-N ChIP biol ×3 PROSER1 knockout mESC TET2-N ChIP biol ×3 wildtype mESC PROSER1-N ChIP biol ×2 PROSER1 knockout mESC PROSER1-N ChIP biol ×2 +10 more

Supports a case/control comparison: 15 samples read as cases, 18 as controls.

How we read this: 17 replicated groups read from 41 sample titles; they account for 40 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

+ 1 more — browse all 41 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq 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.