GEO series

Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers

GSE278245 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 21 samples Submitted 2024/12/21 Platform GPL24676Platform GPL18573

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 21 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: 21 samples: 21 samples, each with a distinct title — no replicated groupsGroups 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: Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancersNature communications · 2025

Summary (written by the submitters)

Cis-regulatory elements (CREs), such as enhancers and promoters, are fundamental regulators of gene expression and, across different cell types, the MYC locus utilizes a diverse regulatory architecture driven by multiple CREs. To better understand differences in CRE function, we performed pooled CRISPR inhibition (CRISPRi) screens to comprehensively probe the 2.8Mb topologically-associated domain containing MYC in 6 human cancer cell lines with nucleotide resolution.

Read the full summary ↓

We map 32 CREs where inhibition leads to changes in cell growth, including 8 that overlap previously identified enhancers. Targeting specific CREs decreased MYC expression by as much as 60%, and cell growth by as much as 50%. Using 3-D enhancer contact mapping, we found that these CREs almost always contact MYC but less than 10% of total MYC contacts impact growth when silenced, highlighting the utility of our approach to identify phenotypically-relevant CREs. We also detect an enrichment of lineage-specific transcription factors (TFs) at MYC CREs and, for some of these TFs, find a strong, tumor-specific correlation between TF and MYC expression not found in normal tissue. Taken together, these CREs represent systematically identified, functional regulatory regions and demonstrate how the same region of the human genome can give rise to complex, tissue-specific gene regulation.

Published in

Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers

Caragine CM, Le VT, Mustafa M et al. · Nature communications 2025 · PMID 39948336 · doi:10.1038/s41467-025-56568-5

This dataset

Open GSE278245 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 GSE278245_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 PRJNA1166205 and SRA study SRP535333. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39948336) ↗

Study design

21 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 21 sample titles: 21 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

GSM8542513 A375, Replicate1, H3K27ac HiChIP
GSM8542514 A375, Replicate2, H3K27ac HiChIP
GSM8542515 A549, Replicate1, H3K27ac HiChIP
GSM8542516 A549, Replicate2, H3K27ac HiChIP
GSM8542517 HT29, Replicate1, H3K27ac HiChIP
GSM8542518 HT29, Replicate2, H3K27ac HiChIP
GSM8542519 MDAMB231, Replicate1, H3K27ac HiChIP
GSM8542520 MDAMB231, Replicate2, H3K27ac HiChIP
GSM8542521 K562, Replicate1, H3K27ac HiChIP
GSM8542522 K562, Replicate2, H3K27ac HiChIP
GSM8542523 PC9, Replicate1, H3K27ac HiChIP
GSM8542524 PC9, Replicate2, H3K27ac HiChIP
GSM8542525 HT29, Cas13 CCAT1 nontargeting guide, Replicate1, H3K27ac HiChIP
GSM8542526 HT29, Cas13 CCAT1 nontargeting guide, Replicate2, H3K27ac HiChIP
GSM8542527 HT29, Cas13 CCAT1 nontargeting guide, Replicate3, H3K27ac HiChIP
GSM8542528 HT29, Cas13 CCAT1 targeting guide1, Replicate1, H3K27ac HiChIP
GSM8542529 HT29, Cas13 CCAT1 targeting guide1, Replicate2, H3K27ac HiChIP
GSM8542530 HT29, Cas13 CCAT1 targeting guide1, Replicate3, H3K27ac HiChIP
GSM8542531 HT29, Cas13 CCAT1 targeting guide2, Replicate1, H3K27ac HiChIP
GSM8542532 HT29, Cas13 CCAT1 targeting guide2, Replicate2, H3K27ac HiChIP
GSM8542533 HT29, Cas13 CCAT1 targeting guide2, Replicate3, H3K27ac HiChIP

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