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Pharmacological Modulation of BMAL1 Alters Circadian Dynamics and the Macrophage Immune Response

GSE255357 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2025/02/03 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 36 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
Mus musculus (mouse)
Samples
36 samples: 8 conditions, mostly with about 6 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.
Paper
Pharmacological targeting of BMAL1 modulates circadian and immune pathwaysNature chemical biology · 2025
Summary (written by the submitters)
The master transcription factor BMAL1-CLOCK is crucial for orchestrating rhythmic gene expression and governing circadian rhythms. Pharmacological manipulation of this central circadian regulator requires accessible protein cavities and selective compounds. By targeting BMAL1 through a resident cavity in its PAS-B domain, we demonstrate that the small-molecule Core Circadian Modulator (CCM) penetrates and substantially expands this pocket.
Read the full summary ↓
Biochemical and cellular analyses validate CCM's target engagement selectivity, enabling direct access to BMAL1's transcriptional activities. CCM induces dose-dependent changes in PER2-Luc macrophage oscillations and selectively modifies expression patterns of circadian controlled genes. In activated macrophages, CCM modulates BMAL1-CLOCK controlled inflammatory and phagocytic pathways to promote their downregulation. Our findings demonstrate the feasibility of directly targeting BMAL1-CLOCK as a strategy for circadian regulation and targeting circadian-regulated processes
Published in
Pharmacological targeting of BMAL1 modulates circadian and immune pathways
Pu H, Bailey LC, Bauer LG et al. · Nature chemical biology 2025 · PMID 40133642 · doi:10.1038/s41589-025-01863-x
This dataset
Open GSE255357 in finder → Find more mouse 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 GSE255357_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 PRJNA1074737 and SRA study SRP488936. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40133642) ↗
Study design
8 conditions, mostly with about 6 replicates each
BMDM, Bmal1-KO, LPS, ×6 BMDM, Bmal1-KO, CCM, ×6 BMDM, Bmal1-KO, LPS + CCM, ×6 BMDM, Bmal1-KO, Vehicle control, ×6 BMDM, Wild-type, LPS, ×3 BMDM, Wild-type, CCM, ×3 BMDM, Wild-type, LPS + CCM, ×3 BMDM, Wild-type, Vehicle control, ×3

Supports a between-group comparison across 36 samples.

How we read this: 8 replicated groups read from 36 sample titles; they account for 36 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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