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Characterization of human CD34+ HSPC-derived neutrophils with limited myeloid-derived immunosuppressive cell activity

GSE300707 Homo sapiens (human) RNA-seq (gene expression) 46 samples Submitted 2025/08/09 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 46 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
Homo sapiens (human)
Samples
46 samples: 10 conditions, mostly with about 4 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.
Paper
Characterization of human CD34(+) HSPC-derived neutrophils with limited myeloid-derived immunosuppressive cell activityiScience · 2025
Summary (written by the submitters)
Neutrophils have limited utility as a fundamental research model and transfusion product due to their short lifespan. Here, we cultured CD34+ hematopoietic stem and progenitor cell (HSPC)-derived neutrophils and compared them to peripheral blood neutrophils in terms of morphology, phenotype, and function. Our culture system resulted in morphologically mature CD15+CD11b+CD16high neutrophils with effector functions almost indistinguishable from blood neutrophils, confirmed by a high similarity in transcription and protein abundance patterns.
Read the full summary ↓
While exhibiting microbial killing capacity and antibody-dependent cellular cytotoxicity, these cells were deficient in myeloid-derived suppressor cell activity. This deficiency in immunosuppressive activity correlated with a distinct granular composition in comparison to blood neutrophils, instead of immunosuppressive characteristics that are currently held to define neutrophil-MDSC phenotype. Taken together, our cultured neutrophils closely resemble blood neutrophils, offering a repository for fundamental research and a step toward an effective transfusion product with limited immunosuppressive activity as a functional property.
Published in
Characterization of human CD34(+) HSPC-derived neutrophils with limited myeloid-derived immunosuppressive cell activity
Webbers SDS, Gankema AAF, van Oosterom F et al. · iScience 2025 · PMID 41054507 · doi:10.1016/j.isci.2025.113404
This dataset
Open GSE300707 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 GSE300707_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 PRJNA1281696 and SRA study SRP594361. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41054507) ↗
Study design
10 conditions, mostly with about 4 replicates each
Hematopoietic stem cell; Day 0; ×6 Stem-Line II; Day 17; CD16 positive; ×6 Blood neutrophils; ×6 Stem-Line II; Day 14; CD16 positive; ×5 Stem-Line II; Day 10; Bulk cells; ×4 Stem-Line II; Day 14; Bulk cells; ×4 Stem-Line II; Day 14; CD16 negative; ×4 Stem-Line II; Day 17; Bulk cells; ×4 +2 more

Supports a between-group comparison across 46 samples.

How we read this: 10 replicated groups read from 46 sample titles; they account for 46 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

+ 6 more — browse all 46 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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