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Differential genome-wide profile of histone modifications upon treatment with gamma-secretase inibithor (GSI) DAPT [ChIP-seq]

GSE254806 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 57 samples Submitted 2024/03/24 Platform GPL17021
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 57 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
57 samples: 27 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
Comprehensive genomic features indicative for Notch responsivenessNucleic acids research · 2024
Summary (written by the submitters)
The Notch signaling pathway regulates several processes including development and differentiation and its aberrant regulation leads to several diseases. Here, we investigated the differential chromatin accessibility, genome-wide distribution of the transcription factor RBPJ and the differential regulation of H3K4me1 and H3K4me3 upon pharmacological inhibition of the Notch pathway with gamma-secretase inibibitor (GSI) DAPT in mouse pre-T (Beko) cells.
Published in
Comprehensive genomic features indicative for Notch responsiveness
Giaimo BD, Friedrich T, Ferrante F et al. · Nucleic acids research 2024 · PMID 38647081 · doi:10.1093/nar/gkae292
This dataset
Open GSE254806 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 GSE254806_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 PRJNA1071991 and SRA study SRP487369. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38647081) ↗
Study design
27 conditions, mostly in duplicate
Beko_24h_DMSO_H3K36me1_batch2 ×2 Beko_24h_DMSO_H3K9me1_batch3 ×2 Beko_24h_DMSO_H3K36me2_batch2 ×2 Beko_24h_DMSO_H3K9me2_batch1 ×2 Beko_24h_DMSO_H3K36me3_batch2 ×2 Beko_24h_DMSO_H3K9me3_batch1 ×2 Beko_24h_DMSO_H3K9ac_batch2 ×2 Beko_24h_DMSO_H3K18ac_batch2 ×2 +22 more

Supports a between-group comparison across 54 samples.

How we read this: 27 replicated groups read from 57 sample titles; they account for 54 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

+ 17 more — browse all 57 samples with per-sample file links →

Datasets on a similar topic

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

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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.