GEO series

Systemic Inflammation Impairs Human Myelopoiesis [bulkRNA-Seq]

GSE212091 Homo sapiens (human) Single-cell RNA-seq 30 samples Submitted 2025/03/15 Platform GPL18573

At a glance

Single-cell RNA-seq · human · 30 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: 30 samples: 30 samples, each with a distinct title — no replicated groupsGroups 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: Systemic inflammation impairs myelopoiesis and interferon type I responses in humansNature immunology · 2025

Summary (written by the submitters)

Systemic inflammation (SI) is a prevalent condition with a high mortality rate1. Survivors of hyperinflammatory state of SI frequently enter a long-lasting immunosuppressive state2 deteriorating their life quality3,4. Due to the extensive heterogeneity in SI etiology, the underlying mechanisms are not well understood. Here, we characterized the short and long-term effects of lipopolysaccharide (LPS)-induced SI (LPS-SI, also called endotoxemia5) on blood monocytes and bone marrow (BM) cells.

Read the full summary ↓

Similar to clinical features of SI, we observed a profound but transient acute LPS response, followed by a long-term immunosuppressed state. Single-cell transcriptomic analysis of LPS-SI acute phase unveiled the loss of BM monocytes and the appearance of an inflammatory monocyte-like (i-Mono’s) population, expressing gene programs similar to a cell state identified in early-stage sepsis patients6. We observed impairment of myelopoiesis one week after LPS-SI manifested by a significant loss of intermediate and non-classical monocytes which is associated with reduced expression of interferon type I (IFN-I) genes. We confirm that this compromised myelopoiesis also happens in late-stage sepsis patients. Importantly, IFNb treatment reverted the LPS-induced immunosuppression in monocytes. Our results deepened the knowledge about SI and its long-lasting effects on myelopoiesis, substantiating the importance of IFN-I in the pathophysiology of SI-induced immunosuppression.

Published in

Systemic inflammation impairs myelopoiesis and interferon type I responses in humans

Keramati F, Leijte GP, Bruse N et al. · Nature immunology 2025 · PMID 40251340 · doi:10.1038/s41590-025-02136-4

This dataset

Open GSE212091 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 GSE212091_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 PRJNA873949. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40251340) ↗

Study design

30 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 30 sample titles: 30 distinct titles with little repetition. 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

GSM6509112 Subject1_Baseline
GSM6509113 Subject1_Baseline_exvivo_4h_LPS
GSM6509114 Subject1_4h
GSM6509115 Subject1_4h_exvivo_4h_LPS
GSM6509116 Subject1_8h
GSM6509117 Subject1_8h_exvivo_4h_LPS
GSM6509118 Subject1_24h
GSM6509119 Subject1_24h_exvivo_4h_LPS
GSM6509120 Subject1_7d
GSM6509121 Subject1_7d_exvivo_4h_LPS
GSM6509122 Subject2_Baseline
GSM6509123 Subject2_Baseline_exvivo_4h_LPS
GSM6509124 Subject2_4h
GSM6509125 Subject2_4h_exvivo_4h_LPS
GSM6509126 Subject2_8h
GSM6509127 Subject2_8h_exvivo_4h_LPS
GSM6509128 Subject2_24h
GSM6509129 Subject2_24h_exvivo_4h_LPS
GSM6509130 Subject2_7d
GSM6509131 Subject2_7d_exvivo_4h_LPS
GSM6509132 Subject3_Baseline
GSM6509133 Subject3_Baseline_exvivo_4h_LPS
GSM6509134 Subject3_4h
GSM6509135 Subject3_4h_exvivo_4h_LPS
GSM6509136 Subject3_8h
GSM6509137 Subject3_8h_exvivo_4h_LPS
GSM6509138 Subject3_24h
GSM6509139 Subject3_24h_exvivo_4h_LPS
GSM6509140 Subject3_7d
GSM6509141 Subject3_7d_exvivo_4h_LPS

Datasets on a similar topic

GSE212092 Systemic Inflammation Impairs Human Myelopoiesis [scRNA-Seq] 18 samples shares myelopoiesis, systemic, impairs
GSE276755 Systemic and breast chronic inflammation and hormone disposition promote a tumor-permissive environment for breast cancer in older women (Human Bulk RNA-Seq) 168 samples shares systemic
GSE239775 Quantification of Systemic Inflammation by a Gene Score Uncovers Relevant Features on Acutely Decompensated Cirrhosis 1177 samples shares systemic
GSE278330 Systemic IL-23 blockade downregulates IL-23 receptor-expressing Type 17 T-cell subsets and upregulates regulatory gene expression in myeloid cells in human psoriasis skin 63 samples shares systemic
GSE308252 Exercise intensity differentially modulates systemic molecular responses and predicted interorgan communication in humans 62 samples shares systemic
GSE283597 LINE-1 transposable elements regulate the exit of human pluripotency and early brain development [bulkRNA-seq] 45 samples shares bulkrna-seq
GSE260777 Cloning and comparison of human P63+ progenitor cells from various lung diseases [bulkRNA-seq] 44 samples shares bulkrna-seq
GSE233916 Mutant Huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure 36 samples shares impairs

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.