GEO series

P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease [RNAseq_sgCMPK2]

GSE318651 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/02/10 Platform GPL34290

At a glance

RNA-seq (gene expression) · mouse · 12 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: 12 samples: 3 × Control_sg_Cmpk2 vs 3 × Control_sg_Rosa26 vs 3 × Sen_sg_Cmpk2 vs 3 × Sen_sg_Rosa26Groups 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: p21(+)TREM2(+) senescent macrophages fuel inflammaging and metabolic dysfunction-associated steatotic liver diseaseNature aging · 2026

Summary (written by the submitters)

Cellular senescence drives chronic sterile inflammation during aging via the senescence-associated secretory phenotype (SASP); however, the cell types responsible for this pathology remain poorly defined. Here, we identify p21⁺Trem2⁺ senescent macrophages as a major source of inflammaging. Using primary mouse and human macrophages, we developed a model of DNA damage and cholesterol-induced senescence and applied multi-omic profiling to fully characterize senescent macrophages.

Read the full summary ↓

We found that senescent macrophages exhibit a distinctive p21-TREM2 expression profile and SASP, driven in part by type-I interferon signaling via secreted mitochondrial DNA. We also found that senescent macrophage accumulation occurs in aged and MASLD mouse livers and is enriched in human cirrhotic liver tissue. Finally, senolytic treatment targeting senescent macrophages reduced liver inflammation and steatosis in both aged and MASLD mice. Together, these findings establish macrophage senescence as a central driver of chronic inflammation in aging and metabolic liver disease, highlighting a promising, tractable therapeutic target.

Published in

p21(+)TREM2(+) senescent macrophages fuel inflammaging and metabolic dysfunction-associated steatotic liver disease

Salladay-Perez IA, Avila I, Estrada L et al. · Nature aging 2026 · PMID 41991686 · doi:10.1038/s43587-026-01101-6

This dataset

Open GSE318651 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 GSE318651_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 PRJNA1416426 and SRA study SRP672088. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41991686) ↗

Study design

3 × Control_sg_Cmpk2 vs 3 × Control_sg_Rosa26 vs 3 × Sen_sg_Cmpk2 vs 3 × Sen_sg_Rosa26

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM9499989 Control_sg_Cmpk2_1 Control_sg_Cmpk2
GSM9499990 Control_sg_Cmpk2_2 Control_sg_Cmpk2
GSM9499991 Control_sg_Cmpk2_3 Control_sg_Cmpk2
GSM9499992 Control_sg_Rosa26_4 Control_sg_Rosa26
GSM9499993 Control_sg_Rosa26_5 Control_sg_Rosa26
GSM9499994 Control_sg_Rosa26_6 Control_sg_Rosa26
GSM9499995 Sen_sg_Cmpk2_7 Sen_sg_Cmpk2
GSM9499996 Sen_sg_Cmpk2_8 Sen_sg_Cmpk2
GSM9499997 Sen_sg_Cmpk2_9 Sen_sg_Cmpk2
GSM9499998 Sen_sg_Rosa26_10 Sen_sg_Rosa26
GSM9499999 Sen_sg_Rosa26_11 Sen_sg_Rosa26
GSM9500000 Sen_sg_Rosa26_12 Sen_sg_Rosa26

Datasets on a similar topic

GSE319035 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease [NAFLD_time_course] 77 samples shares trem2, p21, dysfunction-associated, inflammaging, macrophages, senescent, steatotic
GSE318801 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease. 20 samples shares trem2, p21, dysfunction-associated, inflammaging, macrophages, senescent, steatotic
GSE318804 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease. [macro_senescence] 12 samples shares trem2, p21, dysfunction-associated, inflammaging, macrophages, senescent, steatotic
GSE318802 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease. [Trem2ko] 12 samples shares trem2, p21, dysfunction-associated, inflammaging, macrophages, senescent, steatotic
GSE318652 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease [RNAseq_MASHABT263] 11 samples shares trem2, p21, dysfunction-associated, inflammaging, macrophages, senescent, steatotic
GSE205592 Obesity-instructed TREM2-high macrophages identified by comparative analysis of diabetic mouse and human kidney at single-cell resolution [scRNA-seq: DKD_mouse] 41 samples shares trem2, macrophages
GSE278527 Clearance of p21-highly-expressing senescent cells accelerates cutaneous wound healing 36 samples shares p21, senescent
GSE262811 Lack of TREM2 during anti-PD-1 therapy reprograms intestinal macrophages and microbiota to enhance tumor rejection 32 samples shares trem2, macrophages

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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.