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RNA Polymerase II Transcriptional Pausing and Release Regulates Circadian Transcription

GSE287141 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 219 samples Submitted 2026/01/15 Platform GPL19057Platform GPL17021
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 219 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
Mus musculus (mouse)
Samples
219 samples: 17 conditions, mostly with about 12 replicates eachGroups 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.
Summary (written by the submitters)
Circadian rhythms regulate the harmonized gene expression, metabolism and physiology through transcriptional controls. It is widely accepted that the recruitment of circadian transcriptional factors has a critical role in rhythmic gene expressions. However, the roles of RNA polymerase II pausing and release (RNAP II P/R) on circadian rhythm remain largely unknown.
Read the full summary ↓
From the massive and precise sequencing experiments, we found the static occupancies of RNAP II complex on the initiation sites and rhythmic elongation controls on Alas1 and Srebf1 genes. The subsequent genome-wide analysis retrieved 54 circadian RNAP II P/R rhythmic genes (91 transcripts) that are closely related to nutritional signals. Those genes kept unique rhythms in clock mutant mice and showed the dynamic responses under the reversed feeding regime. Here, we report a novel circadian transcription mechanism, RNAP II pausing & rhythmic release.
This dataset
Open GSE287141 in finder → Find more mouse 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 GSE287141_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 PRJNA1211175 and SRA study SRP557650. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
17 conditions, mostly with about 12 replicates each
WT_RNAP_II_CT ×12 WT_8WG16_CT ×12 WT_SER5P_CT ×12 WT_SER7P_CT ×12 WT_SER2P_CT ×12 WT_NELF-E_CT ×12 WT_SPT5_CT ×12 WT_PAF1_CT ×12 +24 more

Supports a between-group comparison across 204 samples.

How we read this: 17 replicated groups read from 219 sample titles; they account for 204 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

+ 179 more — browse all 219 samples with per-sample file links →

Datasets on a similar topic

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.