← BioTransfer GEO Dataset Finder
GEO series

Dependence of RBPJ genomic binding on the formation of macromolecular complexes

GSE249973 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 54 samples Submitted 2025/01/08 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 54 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
54 samples: 20 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
Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA bindingNature communications · 2025
Summary (written by the submitters)
RBPJ is the central transcription factor involved in the Notch-dependent transcriptional response. Ist repressive function is strongly dependent on its interaction with the corepressor SHARP. Here we analyzed the gomic binding of RBPJ wt, and different RBPJ mutants making use of RBPJ or SHARP depleted HeLa cells. and
Published in
Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA binding
Huynh D, Hoffmeister P, Friedrich T et al. · Nature communications 2025 · PMID 39893191 · doi:10.1038/s41467-025-56515-4
This dataset
Open GSE249973 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 GSE249973_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 PRJNA1051531 and SRA study SRP477537. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39893191) ↗
Study design
20 conditions, mostly in duplicate
Input_KO ×2 Input_SHARP_KO ×2 RBPJ_KO_42 ×2 RBPJ_KO_42_Halo ×2 RBPJ_KO_42_HaloRBPJ_FL_AA ×2 RBPJ_KO_42_HaloRBPJ_K195E ×2 RBPJ_KO_42_HaloRBPJ_KRS ×2 RBPJ_KO_42_HaloRBPJ_R218H ×2 +26 more

Supports a between-group comparison across 40 samples.

How we read this: 20 replicated groups read from 54 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

+ 14 more — browse all 54 samples with per-sample file links →

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.