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KAS-CUT&Tag for direct mapping of transcription bubbles

GSE317877 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 122 samples Submitted 2026/07/21 Platform GPL34281
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 122 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
122 samples: 122 samples, each with a distinct title — no replicated groupsGroups 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
KAS-CUT&Tag for direct mapping of transcription bubblesbioRxiv : the preprint server for biology · 2026
Summary (written by the submitters)
We introduce KAS-CUT&Tag, a method that combines N3-kethoxal labeling of exposed guanines with CUT&Tag to directly map Pol II at transcription bubbles. Pol II-induced bubbles are enriched at many highly-expressed genes, but the highest enrichment is at canonical histone genes in all phases of the cell cycle.
Published in
KAS-CUT&Tag for direct mapping of transcription bubbles
Wu W, Greene JE, Ahmad K et al. · bioRxiv : the preprint server for biology 2026 · PMID 42239153 · doi:10.64898/2026.05.15.725569
This dataset
Open GSE317877 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 GSE317877_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 PRJNA1415749 and SRA study SRP668948. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42239153) ↗
Study design
122 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 122 sample titles: 122 distinct titles with little repetition. 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

+ 82 more — browse all 122 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.