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scRNA-seq of bone marrow and splenic emergency granulopoiesis

GSE317310 Mus musculus (mouse) Single-cell RNA-seq 20 samples Submitted 2026/04/17 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 20 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Mus musculus (mouse)
Samples
20 samples: 8 conditions, mostly in duplicateGroups 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
Divergent granulopoiesis at extramedullary sites safeguards antibacterial host defenseScience immunology · 2026
Summary (written by the submitters)
We performed scRNA-seq analysis using the 10X genomics platform of mice following a model of extramedullary hematopoiesis or control. Here, we isolated bone marrow, spleen and blood Gr1+and cKit+-enriched cells to investigate the dynamics of production across both sites of origin.
Read the full summary ↓
In addition, we performed the following treatments and blood cells were sorted following similar strategy: (1) Splenectomy: a group of mice was subjected to splenectomy before CPM/AMD treatment; (2) partial irradiation with a shield protecting the abdominal region of the mouse followed by CPM/AMD treatment; (3) Mice treated with CPM/AMD were administered with anti-CXCR2 depleting antibody.
Published in
Divergent granulopoiesis at extramedullary sites safeguards antibacterial host defense
Silvestre-Roig C, Chevre R, Farjia M et al. · Science immunology 2026 · PMID 41996475 · doi:10.1126/sciimmunol.adw7077
This dataset
Open GSE317310 in finder → Find more mouse 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 GSE317310_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 PRJNA1406717 and SRA study SRP665624. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41996475) ↗
Study design
8 conditions, mostly in duplicate
Surface_Protein_Blood and Organ 1, Saline tre… ×2 Surface_Protein_Bone Marrow and Spleen, Salin… ×2 Surface_Protein_Blood and Organ 1, CPM/AMD tr… ×2 Surface_Protein_Bone Marrow and Spleen, CPM/A… ×2 RNA_Blood and Organ 1, Saline treatment and T… ×2 RNA_Bone Marrow and Spleen, Saline treatment … ×2 RNA_Blood and Organ 1, CPM/AMD treatment and … ×2 RNA_Bone Marrow and Spleen, CPM/AMD treatment… ×2 +4 more

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 20 sample titles; they account for 16 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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