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Single cell transcriptional profiling of monocytes from asthma patients show a predisposition for an inflammatory response

GSE288147 Homo sapiens (human) Single-cell RNA-seq 16 samples Submitted 2025/09/01 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 16 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 16 samples: 6 × A vs 4 × B vs 3 × CGroups 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)

Background: Asthma is the most common chronic lung disorder among children and young adults worldwide. Standard of care therapies are only partially effective and have side effects. Despite highly effective new biologic therapies, ~10% of patients continue to be poorly controlled. Methods. We isolated monocytes from peripheral blood obtained from an asthma patient who received an infusion of interferon γ-activated mesenchymal stromal cells (γMSCs), before and at 15 and 35 days after the infusion.

Read the full summary ↓

We similarly isolated blood monocytes from otherwise healthy subjects with asthma and healthy controls for comparison. We interrogated the monocyte samples with single cell RNA sequencing followed by data analysis using the Seurat pipeline. Findings: A single infusion of γMSCs induced a profound change in circulating monocyte gene expression, including reduction of HLA Class I expression and reduction of gene expression associated with type 1 and type 3 interferon signaling. Further examination of CD14+ and CD16+ monocytes from asthma patients revealed higher expression of proinflammatory genes compared to healthy controls, most notably increased expression of interferon response pathway genes. Within the asthma patients, several viral and interferon response pathways were significantly enriched in severe versus mild asthma. Interpretation: Circulating monocytes from asthma patients may be intrinsically programmed with a dysregulated interferon response. Monocyte directed therapy may be beneficial, especially for patients who are poorly controlled on currently available therapy. Finally, our data suggest that additional studies of γMSC therapy for patients with poorly controlled asthma is warranted.

This dataset

Open GSE288147 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 GSE288147_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 PRJNA1216280 and SRA study SRP560233. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 × A vs 4 × B vs 3 × C

Supports a between-group comparison across 13 samples.

How we read this: 3 replicated groups read from 16 sample titles; they account for 13 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

GSM8759880 Mononuclear cells, pre-infusion
GSM8759881 Mononuclear cells, 15 days post gMSC infusion
GSM8759882 Mononuclear cells, 35 days post gMSC infusion
GSM8759883 A01 A
GSM8759884 A02 A
GSM8759885 A03 A
GSM8759886 A04 A
GSM8759887 A05 A
GSM8759888 A06 A
GSM8759889 B02 B
GSM8759890 B03 B
GSM8759891 B04 B
GSM8759892 B05 B
GSM8759893 C02 C
GSM8759894 C03 C
GSM8759895 C04 C

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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.