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A rewired myeloid niche in spleen establishes stress erythropoiesis

GSE288200 Mus musculus (mouse) Single-cell RNA-seq 9 samples Submitted 2026/03/27 Platform GPL34290Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 9 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
Mus musculus (mouse)
Samples
9 samples: 9 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.
Summary (written by the submitters)
The bone marrow is responsible for steady-state erythropoiesis. However, during emergencies, the erythropoietic function can shift to the spleen. It remains unclear how the spleen, which typically performs erythrocyte recycling, can rapidly switch to become a site for erythropoiesis in stress states. We utilized single-cell sequencing and spatial transcriptomic sequencing to compare changes in myeloid and erythroid cells in the bone marrow and spleen, thereby elucidating the key components of the extramedullary erythropoietic niche.
Read the full summary ↓
We discovered that inflammation can rewire pre-existing macrophages in the spleen, establishing a novel myeloid microenvironment essential for extramedullary erythropoiesis.
This dataset
Open GSE288200 in finder → Find more mouse 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 GSE288200_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 PRJNA1216566 and SRA study SRP560389. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
9 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 9 sample titles: 9 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
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.