GEO series

Circulating immune cell signature analysis in HFpEF across species [RNA-Seq - human]

GSE298173 Homo sapiens (human) Single-cell RNA-seq 18 samples Submitted 2025/07/28 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 18 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: Homo sapiens (human)
Samples: 18 samples: 6 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: Circulating Immune Cell Signature Analysis in HFpEF Across SpeciesCirculation research · 2025

Summary (written by the submitters)

Background: HFpEF is a heterogeneous clinical picture that is closely related to extracardiac comorbidities such as obesity, hypertension and diabetes and is associated with chronic, low-grade systemic inflammation. Previous studies on myocardial biopsies of HFpEF patients showed intramyocardial inflammatory activity, suggesting that the inflammatory processes in HFpEF are predominantly systemic and exhibit compartment specific-patterns.

Read the full summary ↓

Methods: We performed single cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) of HFpEF patients (n=6), HFrEF patients (n=8) and healthy controls (n=7) taking obesity status into account. For validation, bulk RNA sequencing was performed on whole blood samples. In parallel, the systemic immune cell response was investigated in a HFpEF mouse model (induced by a high-fat diet plus L-NAME), with one group additionally administered the anti-inflammatory agent nitro-oleic acid (NO₂-OA). Results: Analysis of human PBMCs revealed a HFpEF-specific inflammatory fingerprint, which manifested in obesity-related increased expression of cytokine signaling genes (e.g. CCL2, TNF) and obesity-independent increases in mitochondrial-associated activity. In the mouse model, HFpEF animals showed a comparable increase in inflammatory markers, with treatment with NO₂-OA leading to a partial normalization of immunological signatures and a significant improvement in diastolic function. Conclusion: Our results demonstrate that the immune cells of patients with HFpEF are characterized by a distinct transcriptional immune signature that differs from that of patients with HFrEF. The conserved immunological signatures between humans and mice, and the beneficial effect of NO₂-OA in a preclinical model, provide important translational insights and generate hypotheses for personalized interventions in HFpEF.

Published in

Circulating Immune Cell Signature Analysis in HFpEF Across Species

Kneuer JM, Müller M, Erbe S et al. · Circulation research 2025 · PMID 40709473 · doi:10.1161/CIRCRESAHA.125.326249

This dataset

Open GSE298173 in finder → Find more human 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 GSE298173_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 PRJNA1268463 and SRA study SRP587883. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40709473) ↗

Study design

6 conditions, mostly in triplicate

RNA-Seq, PBMCs, Vehicle + untreated ×3 RNA-Seq, PBMCs, NO2-OA [1µM] + untreated ×3 RNA-Seq, PBMCs, NO2-OA [3µM] + untreated ×3 RNA-Seq, PBMCs, Vehicle + IL-1β ×3 RNA-Seq, PBMCs, NO2-OA [1µM] + IL-1β ×3 RNA-Seq, PBMCs, NO2-OA [3µM] + IL-1β ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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

GSM9009479 RNA-Seq, PBMCs, Vehicle + untreated 1 RNA-Seq, PBMCs, Vehicle…
GSM9009480 RNA-Seq, PBMCs, Vehicle + untreated 2 RNA-Seq, PBMCs, Vehicle…
GSM9009481 RNA-Seq, PBMCs, Vehicle + untreated 3 RNA-Seq, PBMCs, Vehicle…
GSM9009482 RNA-Seq, PBMCs, NO2-OA [1µM] + untreated 1 RNA-Seq, PBMCs, NO2-OA …
GSM9009483 RNA-Seq, PBMCs, NO2-OA [1µM] + untreated 2 RNA-Seq, PBMCs, NO2-OA …
GSM9009484 RNA-Seq, PBMCs, NO2-OA [1µM] + untreated 3 RNA-Seq, PBMCs, NO2-OA …
GSM9009485 RNA-Seq, PBMCs, NO2-OA [3µM] + untreated 1 RNA-Seq, PBMCs, NO2-OA …
GSM9009486 RNA-Seq, PBMCs, NO2-OA [3µM] + untreated 2 RNA-Seq, PBMCs, NO2-OA …
GSM9009487 RNA-Seq, PBMCs, NO2-OA [3µM] + untreated 3 RNA-Seq, PBMCs, NO2-OA …
GSM9009488 RNA-Seq, PBMCs, Vehicle + IL-1β 1 RNA-Seq, PBMCs, Vehicle…
GSM9009489 RNA-Seq, PBMCs, Vehicle + IL-1β 2 RNA-Seq, PBMCs, Vehicle…
GSM9009490 RNA-Seq, PBMCs, Vehicle + IL-1β 3 RNA-Seq, PBMCs, Vehicle…
GSM9009491 RNA-Seq, PBMCs, NO2-OA [1µM] + IL-1β 1 RNA-Seq, PBMCs, NO2-OA …
GSM9009492 RNA-Seq, PBMCs, NO2-OA [1µM] + IL-1β 2 RNA-Seq, PBMCs, NO2-OA …
GSM9009493 RNA-Seq, PBMCs, NO2-OA [1µM] + IL-1β 3 RNA-Seq, PBMCs, NO2-OA …
GSM9009494 RNA-Seq, PBMCs, NO2-OA [3µM] + IL-1β 1 RNA-Seq, PBMCs, NO2-OA …
GSM9009495 RNA-Seq, PBMCs, NO2-OA [3µM] + IL-1β 2 RNA-Seq, PBMCs, NO2-OA …
GSM9009496 RNA-Seq, PBMCs, NO2-OA [3µM] + IL-1β 3 RNA-Seq, PBMCs, NO2-OA …

Datasets on a similar topic

GSE327707 Sorted bulk RNA-seq profiling of human peripheral blood mononuclear cell populations across diverse in vitro immune stimuli 150 samples shares rna-seq, across
GSE339456 Integrated bulk and spatial transcriptomic analysis identifies progression-associated molecular signatures in biopsy-proven hypertensive nephropathy [RNA-seq] 35 samples shares signature, rna-seq
GSE233321 Single-cell map of the healthy human immune system across the lifespan reveals unique infant immune signatures 118 samples shares signature, across
GSE318490 Single-cell RNA-seq of tumor samples from six advanced HGSOC patients across treatment stages (pre-NACT, post-NACT and platinum-sensitive recurrence) 10 samples shares rna-seq, across
GSE330130 A multi-omics characterization of the human lumbar spinal cord and motor cortex reveals non-overlapping molecular signatures in ALS [snRNA-Seq; snATAC-Seq] 87 samples shares signature, rna-seq
GSE309595 Longitudinal Analysis of Multiple Myeloma: Therapeutic Response and Immune Microenvironment Dynamics in the Context of Tumor Heterogeneity [scRNA-seq] 270 samples shares rna-seq
GSE303271 RNA-seq of liver biopsies from patients with pediatric autoimmune liver disease 64 samples shares rna-seq
GSE334923 Single-cell RNA-seq atlas of peripheral blood and kidney graft immune cells in chronic antibody-mediated rejection 48 samples shares rna-seq

Search all human 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.