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DNA methylation controls unmethylated transcription start sites in the genome in trans

GSE85314 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 39 samples Submitted 2025/07/13 Platform GPL11154Platform GPL13534Platform GPL10558
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: 12 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed expression table (series matrix) and the array files, from NCBI.
Paper
DNA methylation controls unmethylated transcription start sites in the genome in transEpigenomics · 2017
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
DNA methylation controls unmethylated transcription start sites in the genome in trans
Cheishvili D, Christiansen S, Stochinsky R et al. · Epigenomics 2017 · PMID 28470094 · doi:10.2217/epi-2016-0141
This dataset
Open GSE85314 in finder → Find more human methylation 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 GSE85314_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 PRJNA338155 and SRA study SRP081156. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 28470094) ↗
Study design
12 conditions, mostly in triplicate
genomic DNA from NorHep# ×3 genomic DNA from NorHep ShDNMT1# ×3 genomic DNA from HepG2# ×3 genomic DNA from HepG2 ShDNMT1# ×3 genomic DNA from SKHep1# ×3 genomic DNA from SKHep1 ShDNMT1# ×3 total RNA from NorHep ×3 total RNA from HepG2 ×3 +10 more

Supports a between-group comparison across 33 samples.

How we read this: 12 replicated groups read from 39 sample titles; they account for 33 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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