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Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition

GSE235181 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 44 samples Submitted 2025/02/10 Platform GPL21697
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 44 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
44 samples: 22 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
Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transitionNature structural & molecular biology · 2025
Summary (written by the submitters)
Metazoan gene transcription by RNA polymerase (Pol) II is regulated in the promoter-proximal region. Pol II can undergo termination in the promoter-proximal region, but whether this can contribute to transcription regulation in cells remains unclear. Here, we extend our previous multi-omics analysis to quantify changes in transcription kinetics during a human cell type transition event.
Read the full summary ↓
We observe that upregulation of transcription involves an increase in initiation frequency and, at a set of genes, a decrease in promoter-proximal termination. In turn, downregulation of transcription involves a decrease in initiation frequency and an increase in promoter-proximal termination. Thus, promoter-proximal termination of Pol II contributes to the regulation of human gene transcription.
Published in
Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition
Lysakovskaia K, Devadas A, Schwalb B et al. · Nature structural & molecular biology 2025 · PMID 39934431 · doi:10.1038/s41594-025-01486-9
This dataset
Open GSE235181 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 GSE235181_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 PRJNA984722 and SRA study SRP444496. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39934431) ↗
Study design
22 conditions, mostly in duplicate
BLaER1_mNETseq_PolII_0h ×2 BLaER1_mNETseq_PolII_12h ×2 BLaER1_mNETseq_PolII_24h ×2 BLaER1_mNETseq_PolII_72h ×2 BLaER1_mNETseq_PolII_96h ×2 BLaER1_ChIPNexusseq_PolII_DMSO_30_0h ×2 BLaER1_ChIPNexusseq_PolII_DMSO_30_96h ×2 BLaER1_ChIPNexusseq_PolII_DMSO_6_0h ×2 +14 more

Supports a between-group comparison across 44 samples.

How we read this: 22 replicated groups read from 44 sample titles; they account for 44 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

+ 4 more — browse all 44 samples with per-sample file links →

Datasets on a similar topic

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