GEO series

Host aging induces a senescent-like phenotype in neutrophils with altered transcriptional responses to Streptococcus pneumoniae infection

GSE294007 Mus musculus (mouse) RNA-seq (gene expression) 11 samples Submitted 2025/05/01 Platform GPL19057

At a glance

RNA-seq (gene expression) · mouse · 11 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: 11 samples
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)

Streptococcus pneumoniae is a Gram-positive commensal of the nasopharynx and highly virulent opportunistic pathogen in the respiratory tract. Despite the availability of multiple vaccines, S. pneumoniae remains a significant health burden especially in aged adults resulting in higher rates of serious disease progression, hospitalization, and death following infection.

Read the full summary ↓

Polymorphonuclear leukocytes (PMNs) are among the first responders in the lung following S. pneumoniae infection. However, studies have indicated that PMNs of human and murine origin are dysfunctional in aged individuals. To identify mechanisms underlying this dysfunction and if it displays characteristics of immunosenescence previously observed in lymphocytes, we conducted RNA sequencing on PMNs in the lungs of young and old mice at 12 and 24 hours post pulmonary infection with S. pneumoniae. Our analysis indicated significant transcriptomic differences between the young and aged cohorts associated with decreased expression of many genes important for effector function including significant metabolic changes. These metabolic changes indicated that PMNS in the lungs of aged mice fail to upregulate glycolysis, which is necessary for anti-pneumococcal activity. Analysis of the transcription factors that may be regulating these differential transcriptomic changes to pneumococcal infection indicated differential regulation by E2f2 in aged mice, which appears to negatively regulate PMN differentiation. Importantly, analysis of PMNs in aged mice display context dependent senescent-like characteristics. Together this would suggest that in aged hosts PMNs display altered maturation and can adopt a senescent-like phenotype in the periphery, which contributes to defective gene expression changes required for normal anti-pneumococcal effector functions.

This dataset

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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 GSE294007_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 PRJNA1247584 and SRA study SRP577030. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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+ 11 more — browse all 11 samples with per-sample file links →

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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.