← BioTransfer GEO Dataset Finder
GEO series

Immunoregulation of Intrahepatic Bone Marrow Monocyte–Derived Macrophages by Dietary Nitrate Prevents Nonalcoholic Fatty Liver Disease

GSE204856 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/08/05 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 8 conditions, mostly in triplicateGroups 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
Sodium nitrate protects against metabolic syndrome by sialin-mediated macrophage rebalanceSignal transduction and targeted therapy · 2025
Summary (written by the submitters)
Although nonalcoholic fatty liver disease (NAFLD) is one of the leading causes of liver disease worldwide, no efficient treatment has been approved yet. We investigated whether oral nitrate administration prevents development of diet-induced NAFLD in two mouse models. Nitrate exerted its protective effect mainly through rebalancing of pro- and anti-inflammatory bone marrow monocyte–derived macrophages (MoMFs) in the liver.
Read the full summary ↓
Using an NAFLD model in relatively germ-free mice and bone marrow–transplanted mice with a heritable Slc17a5 mutation, we showed that nitrate can prevent NAFLD by direct regulation of MoMFs through sialin, besides via the classical nitric oxide pathway. In vitro studies revealed that nitrate directly regulates mouse and human macrophages through the sialin-Sema4A pathway. Our work demonstrated for the first time nitrate’s ability to prevent NAFLD by directly modulating the homeostasis of hepatic pro- and anti-inflammatory macrophages, which indicates a novel strategy for potential clinical application in NAFLD.
Published in
Sodium nitrate protects against metabolic syndrome by sialin-mediated macrophage rebalance
Li S, Wang Y, Zhang Z et al. · Signal transduction and targeted therapy 2025 · PMID 41034188 · doi:10.1038/s41392-025-02418-1
This dataset
Open GSE204856 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 GSE204856_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 PRJNA842565 and SRA study SRP377175. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41034188) ↗
Study design
8 conditions, mostly in triplicate
M1 ×3 M1+Nit ×3 M2 ×3 M2+Nit ×3 Slc17a5 siRNA-M1 ×3 Slc17a5 siRNA-M1+Nit ×3 Slc17a5 siRNA-M2 ×3 Slc17a5 siRNA-M2+Nit ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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

Search all mouse 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.