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Genome-wide distribution of H3K9me3, RNA polymerase II, Rloop, DDX55 and HA-tagged DDX55 in WT and DDX55 knockout CD4 naive T cells

GSE263249 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 23 samples Submitted 2025/09/01 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 23 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
23 samples: 11 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.
Summary (written by the submitters)
Genome-wide distribution of H3K9me3, RNA polymerase II, Rloop, DDX55 and HA-tagged DDX55 in WT and DDX55 knockout CD4 naive T cells were determined by cleavage under targets and tagmentation (CUT&Tag) assays followed by deep sequencing (CUT&Tag-seq) with corresponding antibodies.
This dataset
Open GSE263249 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 GSE263249_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 PRJNA1096347 and SRA study SRP499826. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
11 conditions, mostly in duplicate
WT_CD4_Naive_H3K9me3_CUT&Tag ×2 DDX55_KO_CD4_Naive_H3K9me3_CUT&Tag ×2 WT_CD4_Naive_PolII_CUT&Tag ×2 DDX55_KO_CD4_Naive_PolII_CUT&Tag ×2 WT_CD4_Naive_Rloop_CUT&Tag ×2 DDX55_KO_CD4_Naive_Rloop_CUT&Tag ×2 WT_CD4_Naive_Rloop_RNaseH_CUT&Tag ×2 DDX55_KO_CD4_Naive_Rloop_RNaseH_CUT&Tag ×2 +4 more

Supports a between-group comparison across 22 samples.

How we read this: 11 replicated groups read from 23 sample titles; they account for 22 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 →

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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.