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Af-CUT&Tag: A Sensitive and Antibody-Free Chromatin Profiling Method Using Genetically Encoded Tags and High-Affinity Binders Fused to Tn5

GSE283706 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 65 samples Submitted 2024/12/15 Platform GPL34284Platform GPL34290
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 65 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
65 samples: 49 distinct titles, 12 of them repeatedGroups 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
Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5Nature communications · 2026
Summary (written by the submitters)
Conventional chromatin profiling techniques are often limited by antibody availability and performance. Here, we introduce Af-CUT&Tag, a target antibody-free method that overcomes these limitations by using CRISPR-integrated peptide tags (HiBiT/ALFA-tag) recognized by engineered binders (LgBiT/NbALFA) fused to a Tn5 transposase. Af-CUT&Tag eliminates dependence on traditional target antibodies, achieving robust specificity and sensitivity with as few as 500 cells.
Read the full summary ↓
It provides high-quality chromatin profiles, with improved signal-to-noise ratios and library quality compared with conventional antibody-based counterparts, while also enabling single-cell resolution (scAf-CUT&Tag). Applying Af-CUT&Tag to Hippo effectors (YAP1/TAZ) during liver regeneration revealed dynamic chromatin remodeling, including YAP1/TAZ-mediated control of lipid metabolism (e.g., Lpin1, Fasn) and heme clearance (Hpx, Trf). We further identify miR-122 as a critical regulator of these processes, impacting liver regeneration. The versatility of Af-CUT&Tag in cell lines, bulk tissues, and single nuclei establishes it as a powerful tool for studying gene regulation in development, disease, and regeneration. Keywords: Antibody-Free CUT&Tag; Chromatin Binding; Epigenetic Profiling; Peptide-binder; Single-cell analysis
Published in
Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5
Wang X, Deng X, Qiu L et al. · Nature communications 2026 · PMID 41547832 · doi:10.1038/s41467-026-68454-9
This dataset
Open GSE283706 in finder → Find more 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 GSE283706_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 PRJNA1195075 and SRA study SRP549873. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41547832) ↗
Study design
49 distinct titles, 12 of them repeated
SW480 cell,KI-CTCT-HiBiT,nano-Tn5_anti-CTCF(n… ×3 SW480 cell,KI-CTCF-ALFA,NbALFA-Tn5(Af-CUT&Tag… ×3 SW480 cell,KI-CTCF-HiBiT,LgBiT-Tn5(Af-CUT&Tag… ×3 SW480 cell,KI-CTCT-HiBiT,nano-Tn5_anti-HiBiT(… ×3 SW480 cell,KI-RPB1-HiBiT,anti-RPB1(CUT&Tag), ×2 SW480 cell,KI-RPB1-HiBiT,LgBiT-Tn5(Af-CUT&Tag… ×2 SW480 cell,KI-RPB1-HiBiT,Nano-Tn5(nano-CUT&Ta… ×2 DLD-1 cell,KI-RPB1-ALFA-tag,NbALFA-Tn5(Af-CUT… ×2 +4 more

How we read this: Read from 65 sample titles: 49 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

+ 25 more — browse all 65 samples with per-sample file links →

Datasets on a similar topic

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

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