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The cortical microenvironment drives early immune organization and controls early osteoclastogenesis in bone healing

GSE305266 Mus musculus (mouse) Single-cell RNA-seq 90 samples Submitted 2025/12/08 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 90 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
90 samples: 90 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)
We employed single-cell RNA sequencing using the 10x Genomics platform to investigate the cellular dynamics and early immune-stromal interactions during fracture healing in young and aged mice. Tissue-resident and infiltrating cell populations were collected from spatially defined bone marrow and cortical compartments from intact femurs as well as day 3 adn day 7 post-osteotomy.
Read the full summary ↓
In totall, over 178,000 cells were profiled without prior enrichment or cell sorting, capturing the full diversity of immune and stromal cells involved in early bone regeneration. This dataset provides a comprehensive, unbiased atlas of the early fracture healing response and offers novel insights into the spatial regulation of osteoclastogenesis and the alterations with age.
This dataset
Open GSE305266 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 GSE305266_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 PRJNA1304961 and SRA study SRP608495. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
90 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 90 sample titles: 90 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

+ 50 more — browse all 90 samples with per-sample file links →

Datasets on a similar topic

Search all mouse 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.