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A bone regenerative strategy based on extracellular vesicles transporting citrate for promoting biomineralization [timepoint]

GSE240536 Mus musculus (mouse) RNA-seq (gene expression) 33 samples Submitted 2025/10/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 33 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
Mus musculus (mouse)
Samples
33 samples: 11 conditions, mostly in triplicateGroups 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 mineralization of extracellular matrix (ECM) rich in collagen is a biological process in many bones. It is well known that organic molecules from the extracellular matrix of mineralized tissues are crucial for constructing apatite minerals. Here we found that differences in cellular metabolic status significantly affect the degree of mineralization.
Read the full summary ↓
The metabolite citrate, as a component of apatite nanocomposites, is crucial to the biomineralization of bones. Citrate is transported to the ECM through extracellular vesicles (EVs) and amorphous calcium phosphate (ACPs). Functionally, citrate can bridge more Ca2+ in EVs, contributing to higher intra-fiber mineralization. EVs produced by cells with active metabolic levels can improve the mineralization of poorly mineralized cells. The results indicate that the content of EVs can reflect the metabolic state of cells, thereby regulating the function of ECM. In general, this work reveals the complex metabolic process as a way to regulate biomineralization and proposes a new form of molecular transport, which provides a new bio-inspired strategy for bone regeneration.
This dataset
Open GSE240536 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 GSE240536_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 PRJNA1004199 and SRA study SRP454438. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
11 conditions, mostly in triplicate
E8.5 ×3 E9 ×3 E9.5 ×3 E10 ×3 E10.5 ×3 E11 ×3 E11.5 ×3 E12 ×3 +3 more

Supports a between-group comparison across 33 samples.

How we read this: 11 replicated groups read from 33 sample titles; they account for 33 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

Search all mouse RNA-seq datasets in GEO →

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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.