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Multiomics Analyses Unveil Immune Landscape in Pediatric and Adult Sepsis [CITE-seq]

GSE279451 Homo sapiens (human) Single-cell RNA-seq 40 samples Submitted 2025/09/28 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 40 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
40 samples: 5 conditions, mostly with about 14 replicates eachGroups 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)
Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated host response to infection. The immune response varies significantly based on the anatomical source of infection. This study uses cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to profile surface protein expression and transcriptomics at the single-cell level in PBMC samples from 40 adults: 3 healthy controls, 5 ICU controls, and 32 sepsis patients.
Read the full summary ↓
The sepsis patients are categorized by infections originating from different anatomical sites. The findings aim to support sepsis stratification and guide the development of targeted therapies based on infection sources.
This dataset
Open GSE279451 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 GSE279451_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 PRJNA1172726. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 conditions, mostly with about 14 replicates each
citeseq Abd-S ×14 citeseq Res-S ×14 citeseq IC ×5 citeseq Uri-S ×4 citeseq HC ×3

Supports a between-group comparison across 40 samples.

How we read this: 5 replicated groups read from 40 sample titles; they account for 40 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
Datasets on a similar topic

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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.