GEO series

Restored clearance of senescent neutrophils by tissue-resident macrophages limits organ aging

GSE319489 Mus musculus (mouse) Single-cell RNA-seq 8 samples Submitted 2026/07/16 Platform GPL34328

At a glance

Single-cell RNA-seq · mouse · 8 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 8 samples: 2 × Mouse liver scRNA-seq, EP2 cKO Aged, biol vs 2 × Mouse liver scRNA-seq, EP2 WT Aged, biol vs 2 × Mouse liver scRNA-seq, EP2 cKO Young, biol vs 2 × Mouse liver scRNA-seq, EP2 WT Young, biolGroups 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.

Summary (written by the submitters)

Single-cell RNA sequencing of sorted mouse liver cells from young (6-8 month) and aged (23-25 month) Cx3cr1CreER;EP2wt/wt (WT) and Cx3cr1CreER;EP2lox/lox (EP2 cKO) male mice. Liver cells were enzymatically dissociated and live CD45+, CD1d+, or CD31+ cells were FACS-sorted in a 1:1:1 ratio, then processed using the 10x Genomics Chromium X platform (Next GEM Single Cell 3' Gene Expression).

Read the full summary ↓

This dataset supports the finding that tissue-resident macrophage (TRM)-selective EP2 (PTGER2) deletion restores efferocytic clearance of senescent neutrophils and reverses age-associated transcriptional programs in Kupffer cells, preventing multi-organ aging phenotypes.

This dataset

Open GSE319489 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 GSE319489_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1423603 and SRA study SRP677032. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

2 × Mouse liver scRNA-seq, EP2 cKO Aged, biol vs 2 × Mouse liver scRNA-seq, EP2 WT Aged, biol vs 2 × Mouse liver scRNA-seq, EP2 cKO Young, biol vs 2 × Mouse liver scRNA-seq, EP2 WT Young, biol

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 8 sample titles; they account for 8 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

GSM9518586 Mouse liver scRNA-seq, EP2 cKO Aged, biol rep 1 Mouse liver scRNA-seq, …
GSM9518587 Mouse liver scRNA-seq, EP2 cKO Aged, biol rep 2 Mouse liver scRNA-seq, …
GSM9518588 Mouse liver scRNA-seq, EP2 WT Aged, biol rep 1 Mouse liver scRNA-seq, …
GSM9518589 Mouse liver scRNA-seq, EP2 WT Aged, biol rep 2 Mouse liver scRNA-seq, …
GSM9518590 Mouse liver scRNA-seq, EP2 cKO Young, biol rep 1 Mouse liver scRNA-seq, …
GSM9518591 Mouse liver scRNA-seq, EP2 cKO Young, biol rep 2 Mouse liver scRNA-seq, …
GSM9518592 Mouse liver scRNA-seq, EP2 WT Young, biol rep 1 Mouse liver scRNA-seq, …
GSM9518593 Mouse liver scRNA-seq, EP2 WT Young, biol rep 2 Mouse liver scRNA-seq, …

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 macrophages, senescent
GSE278527 Clearance of p21-highly-expressing senescent cells accelerates cutaneous wound healing 36 samples shares clearance, senescent
GSE279117 HIF1α deletion promotes mitochondrial repurposing in bone marrow-derived macrophages, but not in tissue-resident alveolar macrophages 24 samples shares tissue-resident, macrophages
GSE318801 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease. 20 samples shares macrophages, senescent
GSE301560 Hematopoietic loss of Y chromosome activates immune checkpoints to impair senescent cell clearance contributing to renal disease 20 samples shares clearance, senescent
GSE282695 STAT3 regulates pathogen control and clearance in macrophages by reprogramming inflammation-induced microbial defense response 18 samples shares macrophages, clearance
GSE318804 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease. [macro_senescence] 12 samples shares macrophages, senescent
GSE318651 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease [RNAseq_sgCMPK2] 12 samples shares macrophages, senescent

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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.