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DNA methylation insulates exons from CTCF loops with nuclear speckles (ChiP-Seq)

GSE217752 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 39 samples Submitted 2024/11/11 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 39 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
39 samples: 19 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.
Paper
DNA methylation insulates genic regions from CTCF loops near nuclear speckleseLife · 2025
Summary (written by the submitters)
CTCF is necessary for the formation and maintenance of many DNA loops and Topologically Associating Domains, but the genomic features that influence CTCF looping are incompletely understood. We characterized the downstream effects of treating cells with a DNMT1 inhibitor and acute depletion of nuclear speckles to study the factors that influence CTCF looping.
Published in
DNA methylation insulates genic regions from CTCF loops near nuclear speckles
Roseman SA, Siegenfeld AP, Lee C et al. · eLife 2025 · PMID 40900123 · doi:10.7554/eLife.102930
This dataset
Open GSE217752 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 GSE217752_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 PRJNA900264 and SRA study SRP407264. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40900123) ↗
Study design
19 conditions, mostly in duplicate
K562wt_DNMT1i_3days_CTCF_ChIP ×2 K562wt_DMSO_3days_CTCF_ChIP ×2 HCT116wt_DNMT1i_3days_CTCF_ChIP ×2 HCT116wt_DMSO_3days_CTCF_ChIP ×2 K562wt_DNMT1i_3days_CTCF_input ×2 K562wt_DMSO_3days_CTCF_input ×2 HCT116wt_DNMT1i_3days_CTCF_input ×2 HCT116wt_DMSO_3days_CTCF_input ×2 +12 more

Supports a between-group comparison across 38 samples.

How we read this: 19 replicated groups read from 39 sample titles; they account for 38 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

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