GEO series

Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering [CHIP-seq]

GSE300307 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 27 samples Submitted 2025/08/15 Platform GPL20301

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 27 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: 27 samples: 26 distinct titles, 1 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: Ectopic Recruitment of the CTCF N-Terminal Domain with Two Proximal Zinc-Finger Domains as a Tool for 3D Genome EngineeringInternational journal of molecular sciences · 2025

Summary (written by the submitters)

We developed a panel of chimeric proteins consisting of either full-length or truncated CTCF fused with programmable DNA-binding module dCas9 and fluorescent tracker EGFP. We found that the recruitment of a chimeric protein based on the CTCF N-terminal domain and two zinc-finger domains to the human HOXD locus leads to the de novo formation of a spatial contact with a nearby cohesin/CTCF-bound region anchoring several chromatin loops.

Read the full summary ↓

This chimeric protein did not show binding to CTCF motifs and did not affect epigenetic and transcription profile of the locus. Recruitment of this chimeric protein is also able to restore chromatin loops, lost after deletion of an endogenous CTCF binding site. Together, our data indicate that the ectopic recruitment of CTCF N-terminal part could be an appropriate tool for the 3D genome engineering.

Published in

Ectopic Recruitment of the CTCF N-Terminal Domain with Two Proximal Zinc-Finger Domains as a Tool for 3D Genome Engineering

Tiukacheva EA, Luzhin AV, Kruglova N et al. · International journal of molecular sciences 2025 · PMID 40806572 · doi:10.3390/ijms26157446

This dataset

Open GSE300307 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 GSE300307_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 PRJNA1280070 and SRA study SRP593535. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40806572) ↗

Study design

26 distinct titles, 1 of them repeated

K562 cells, N+2 CTCF-dCas9-EGFP, ChIP, H3K27m… ×2

How we read this: Read from 27 sample titles: 26 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

GSM9058123 K562 cells, WT, ChIP, CTCF
GSM9058124 K562 cells, WT, ChIP, SMC3
GSM9058125 K562 cells, WT, ChIP, H3K27me3
GSM9058126 K562 cells, dCas9-EGFP, ChIP, H3K27me3
GSM9058127 K562 cells, dCas9-EGFP, ChIP, SMC3
GSM9058128 K562 cells, N CTCF-dCas9-EGFP, ChIP, H3K27me3
GSM9058129 K562 cells, N+2 CTCF-dCas9-EGFP, ChIP, H3K27me3, rep 1
GSM9058130 K562 cells, N+2 CTCF-dCas9-EGFP, ChIP, H3K27me3, rep 2
GSM9058131 K562 cells, N+2 CTCF-dCas9-EGFP, ChIP,SMC3
GSM9058132 K562 cells, N+2 CTCF-dCas9-EGFP, ChIP, EGFP
GSM9058133 K562 cells, N+7 CTCF-dCas9-EGFP, ChIP, H3K27me3
GSM9058134 K562 cells, N+11 CTCF-dCas9-EGFP, ChIP, H3K27me3
GSM9058135 K562 cells, Full CTCF-dCas9-EGFP, ChIP, H3K27me3
GSM9058136 K562 cells, Full CTCF-dCas9-EGFP, ChIP, EGFP
GSM9058137 K562 cells, CBS deletion, ChIP, H3K27me3
GSM9058138 K562 cells, restored CBS + dCas9-EGFP, ChIP, H3K27me3
GSM9058139 K562 cells, restored CBS + N+2 CTCF-dCas9-EGFP, ChIP, H3K27me3
GSM9058140 K562 cells, CBS deletion, Input
GSM9058141 K562 cells, restored CBS + dCas9-EGFP, Input
GSM9058142 K562 cells, restored CBS + N+2 CTCF-dCas9-EGFP, Input
GSM9058143 K562 cells, WT, Input
GSM9058144 K562 cells, dCas9-EGFP, Input
GSM9058145 K562 cells, N CTCF-dCas9-EGFP,Input
GSM9058146 K562 cells, N+2 CTCF-dCas9-EGFP, Input
GSM9058147 K562 cells, N+7 CTCF-dCas9-EGFP, Input
GSM9058148 K562 cells, N+11 CTCF-dCas9-EGFP, Input
GSM9058149 K562 cells, CTCF-dCas9-EGFP, Input

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GSE278192 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T ChIP-seq] 45 samples shares ctcf, chip-seq
GSE217752 DNA methylation insulates exons from CTCF loops with nuclear speckles (ChiP-Seq) 39 samples shares ctcf, chip-seq
GSE188175 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [ChIP-Seq] 28 samples shares ctcf, chip-seq
GSE270784 ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [ChIP-seq] 107 samples shares recruitment, chip-seq

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