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

GSE217759 Homo sapiens (human) DNA methylation 30 samples Submitted 2024/11/11 Platform GPL24676
At a glance

DNA methylation · human · 30 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Homo sapiens (human)
Samples
30 samples: 10 conditions, mostly in triplicateGroups 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 GSE217759 in finder → Find more human RNA-seq 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 GSE217759_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 beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA900270 and SRA study SRP407272. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40900123) ↗
Study design
10 conditions, mostly in triplicate
K562wt_DNMT1i_3days ×3 K562wt_DMSO_3days ×3 HCT116wt_DNMT1i_3days ×3 HCT116wt_DMSO_3days ×3 K562_dtagknockin_dtag13_6hr ×3 K562_dtagknockin_DMSO_6hr ×3 HCT116_HTCTCF_plusHaloPROTAC3_1dayDNMT1i ×3 HCT116_HTCTCF_plusHaloPROTAC3_1dayDMSO ×3 +2 more

Supports a between-group comparison across 30 samples.

How we read this: 10 replicated groups read from 30 sample titles; they account for 30 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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