GEO series

BMAL1 regulates circadian rhythms via phase separation–mediated transcriptional hub formation

GSE325358 Homo sapiens (human) RNA-seq (gene expression) 9 samples Submitted 2026/03/31 Platform GPL34284

At a glance

RNA-seq (gene expression) · human · 9 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Samples: 9 samples: 3 × BMAL1_KO vs 3 × BMAL1_delN90 vs 3 × BMAL1_FLGroups 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: BMAL1 regulates circadian rhythms via phase separation-mediated transcriptional hub formationSignal transduction and targeted therapy · 2026

Summary (written by the submitters)

The mechanisms by which core clock components are spatially organized to ensure robust oscillations in mammals remains unclear. Here, we identify the positive limb factor BMAL1 as a phase-separating protein that forms dynamic biomolecular condensates essential for circadian transcription and behavior. Endogenous BMAL1 forms nuclear punctate that oscillate in sync with the circadian cycle.

Read the full summary ↓

Deletion analysis and optogenetic clustering identify an N_x001E_-terminal 90-amino acid intrinsically disordered region whose phosphorylation state tunes BMAL1 phase separation. Besides, BMAL1 condensates behave as multi-molecular assemblies that selectively recruit CLOCK, P300, MED1, and are specifically promoted by E-box DNA. Functionally, an IDR-deleted BMAL1 mutant fails to rescue rhythmic transcription in Bmal1-KO cells and cannot restore locomotor rhythms when reintroduced into the SCN specific Bmal1‑KO mice. These findings establish BMAL1 condensates as dynamic transcriptional hubs that couple phase separation to circadian rhythm in cells and in vivo.

Published in

BMAL1 regulates circadian rhythms via phase separation-mediated transcriptional hub formation

Gao W, Zhu L, Wei Y et al. · Signal transduction and targeted therapy 2026 · PMID 42062246 · doi:10.1038/s41392-026-02711-7

This dataset

Open GSE325358 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 GSE325358_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1439772 and SRA study SRP685064. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42062246) ↗

Study design

3 × BMAL1_KO vs 3 × BMAL1_delN90 vs 3 × BMAL1_FL

Supports a between-group comparison across 9 samples.

How we read this: 3 replicated groups read from 9 sample titles; they account for 9 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

GSM9601568 BMAL1_KO_rep1 BMAL1_KO
GSM9601569 BMAL1_KO_rep2 BMAL1_KO
GSM9601570 BMAL1_KO_rep3 BMAL1_KO
GSM9601571 BMAL1_delN90_rep1 BMAL1_delN90
GSM9601572 BMAL1_delN90_rep2 BMAL1_delN90
GSM9601573 BMAL1_delN90_rep3 BMAL1_delN90
GSM9601574 BMAL1_FL_rep1 BMAL1_FL
GSM9601575 BMAL1_FL_rep2 BMAL1_FL
GSM9601576 BMAL1_FL_rep3 BMAL1_FL

Datasets on a similar topic

GSE325862 BMAL1 regulates circadian rhythms via phase separation–mediated transcriptional hub formation 36 samples shares bmal1, separation, circadian, formation, mediated, rhythms, phase
GSE326530 Comparative circadian transcriptome analysis reveals dampened and phase-advanced rhythms in sun-exposed skin 160 samples shares circadian, rhythms, phase
GSE243047 METTL3-mediated chromatin contacts promote phase separation during senescence. 22 samples shares separation, mediated, phase
GSE263429 Enhanced Phase Separation Mediated Oncogenicity [ChIP-Seq experiment] 18 samples shares separation, mediated, phase
GSE260643 BMAL1–HIF2A heterodimer modulates circadian variations of myocardial injury 155 samples shares bmal1, circadian
GSE278512 Phase separation of chimeric antigen receptor promotes immunological synapse maturation and persistent cytotoxicity 45 samples shares separation, phase
GSE253091 The Small Extracellular Vesicle-Mediated Intercellular Transformation of CXCR1Low to CXCR1High Tumor Cells Promotes the Progression of Head and Neck Squamous Cell Carcinoma 36 samples shares formation, mediated
GSE253744 Phase separation of phospho-HDAC6 drives aberrant chromatin architecture in triple-negative breast cancer [RNA-seq] 22 samples shares separation, phase

Search all human RNA-seq datasets in GEO →

Share this dataset

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.