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Immunoregulation of Raw264.7 by Nitrate in vitro

GSE248235 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/08/05 Platform GPL13112
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: 6 × M1 vs 6 × M2 vs 6 × Slc17a5 OE M1 vs 6 × Slc17a5 OE M2Groups 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)
Macrophage balance is important in several diseases. Raw 264.7 is a macrophage cell line. We previous detected that sialin (encoded by Slc17a5) play a key role in modulation of Raw264.7 which induced by LPS&IFNγ(M1 cells, proinflammatory cells) or IL4(M2 cells,anti-proinflammatory cells). Results showed nitrate could decrease the pro-inflammatory Raw264.7 cells while increase anti-inflammatory Raw26.7 cells.
Read the full summary ↓
We transfected sialin overexpression plasmid to Raw264.7 and found that sialin could directly modulates Raw264.7 without nitrate. In this study, we want to figure out which genes could be the key factor modulated by sialin.
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 GSE248235 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 GSE248235_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 PRJNA1043071 and SRA study SRP473011. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41034188) ↗
Study design
6 × M1 vs 6 × M2 vs 6 × Slc17a5 OE M1 vs 6 × Slc17a5 OE M2

Supports a between-group comparison across 24 samples.

How we read this: 4 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

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