Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 51 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
- 51 samples: 41 distinct titles, 10 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
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE300308_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1280052 and SRA study SRP593521. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 51 sample titles: 41 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.
- GSM9058099 K562 cells, CTCF-dCas9-EGFP
- GSM9058100 K562 cells, N+11 CTCF-dCas9-EGFP
- GSM9058101 K562 cells, N+7 CTCF-dCas9-EGFP
- GSM9058102 K562 cells, N+2 CTCF-dCas9-EGFP
- GSM9058103 K562 cells, N CTCF-dCas9-EGFP
- GSM9058104 K562 cells, dCas9-EGFP
- GSM9058105 K562 cells, WT, replicate 1
- GSM9058106 K562 cells, WT, replicate 2
- GSM9058107 K562 cells, CBS deletion, replicate 1
- GSM9058108 K562 cells, CBS deletion, replicate 2
- GSM9058109 K562 cells, restored CBS, replicate 1
- GSM9058110 K562 cells, restored CBS, replicate 2
- GSM9058111 K562 cells, WT, RNA-seq, replicate 1
- GSM9058112 K562 cells, WT, RNA-seq, replicate 2
- GSM9058113 K562 cells, N+2 CTCF-dCas9-EGFP, RNA-seq, replicate 1
- GSM9058114 K562 cells, N+2 CTCF-dCas9-EGFP, RNA-seq, replicate 2
- GSM9058115 K562 cells, dCas9-EGFP, RNA-seq, replicate 1
- GSM9058116 K562 cells, dCas9-EGFP, RNA-seq, replicate 2
- GSM9058117 K562 cells, CBS deletion, RNA-seq, replicate 1
- GSM9058118 K562 cells, CBS deletion, RNA-seq, replicate 2
- GSM9058119 K562 cells, restored CBS, N+2, RNA-seq, replicate 1
- GSM9058120 K562 cells, restored CBS, N+2, RNA-seq, replicate 2
- GSM9058121 K562 cells, restored CBS, RNA-seq, replicate 1
- GSM9058122 K562 cells, restored CBS, RNA-seq, replicate 2
- 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
+ 11 more — browse all 51 samples with per-sample file links →
- GSE300307 Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering [CHIP-seq] 27 samples shares ctcf, recruitment, zinc-finger, engineering, n-terminal, proximal, ectopic, domains
- GSE341599 CTCFL(BORIS) contributes to the transcriptional program of ovarian cancer by relaxing CTCF-mediated three-dimensional genome organization 32 samples shares ctcf
- GSE288172 Influence of NIPBL Knockdown-Induced Alterations in Cohesin Loop Extrusion on CTCF Loops, Enhancer-Promoter Connectivity, and PRC Domain Contacts During hESC Differentiation into Pancreatic Lineages 263 samples shares ctcf
- GSE263641 CTCF depletion uncouples the role of enhancer-promoter interactions and higher-order chromatin hubs in gene regulation during cellular differentiation. 137 samples shares ctcf
- GSE215328 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [hESC_H9_d049_ChIP_Seq] 135 samples shares ctcf
- GSE283196 CTCF distribution around AsisI sites in IDHwt and IDHR132H DIvA cells 117 samples shares ctcf
- GSE239270 Investigate FOXA2, NKX2-1, CTCF and P300 cistrome and enhancer (H3K27ac and H3k4me1) reprogramming during NEPC transformation by ChIP-seq. 104 samples shares ctcf
- GSE217760 DNA methylation insulates exons from CTCF loops with nuclear speckles 99 samples shares ctcf
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.