GEO series

Estrogen signaling in PDGFRα+ cells positively regulates cortical bone metabolism via IGFBP5 in female mice.

GSE279051 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2025/12/31 Platform GPL19057

At a glance

Single-cell RNA-seq · mouse · 12 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: 12 samples: 3 × muscle_con vs 3 × muscle_ko vs 3 × bone_con vs 3 × bone_koGroups 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: Estrogen signaling in PDGFRα+ cells positively regulates cortical bone metabolism via IGFBP5 in female miceJBMR plus · 2026

Summary (written by the submitters)

The prevalence of both osteoporosis and sarcopenia increases with age, and 60% of elderly sarcopenia patients also develop osteoporosis. However, the co-occurrence of osteoporosis and sarcopenia remains unclear. We performed single-cell 5’RNA-seq on human skeletal muscle tissues and investigated the enrichment of heritability for musculoskeletal traits in cell type specific cis-regulatory regions.

Read the full summary ↓

We found the fibroblast-specific cis-regulatory regions are highly enriched in the heritability of bone mineral density (BMD). Using GWAS, we identified estrogen receptor α (ESR1) as a common transcription factor that correlated with both BMD and lean mass. We hypothesized that deficiency of estrogen signaling in fibroblast may attenuate musculoskeletal homeostasis. Therefore, we generated mice lacking Esr1 in PDGFRα (a fibroblast marker) + cells (Esr1ΔPα). Although muscle mass and grip strength were not different between groups, distal femoral BMD and cortical thickness were significantly lower in Esr1ΔPα compared to control. Bone histomorphometry showed that cortical bone in Esr1ΔPα exhibited a high turnover bone phenotype. Bulk RNA-seq using PDGFRα+ cells revealed that Igfbp5 expression was significantly higher in Esr1ΔPα compared to control. Furthermore, serum IGFBP5 level was significantly higher in Esr1ΔPα. IGFBP5 treatment in vitro significantly suppressed osteoblast differentiation and facilitated osteoclast differentiation. These results suggest that estrogen signaling in PDGFRα+ cells suppresses Igfbp5 expression, then maintains bone mass, indicating that estrogen signaling in PDGFRα+ cells plays a significant role in bone metabolism.

Published in

Estrogen signaling in PDGFRα+ cells positively regulates cortical bone metabolism via IGFBP5 in female mice

Ikedo A, Aoki R, Sakai H et al. · JBMR plus 2026 · PMID 41496792 · doi:10.1093/jbmrpl/ziaf178

This dataset

Open GSE279051 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 GSE279051_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 PRJNA1170252 and SRA study SRP537247. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41496792) ↗

Study design

3 × muscle_con vs 3 × muscle_ko vs 3 × bone_con vs 3 × bone_ko

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM8560170 muscle_con 1 muscle_con
GSM8560171 muscle_con 2 muscle_con
GSM8560172 muscle_con 3 muscle_con
GSM8560173 muscle_ko 1 muscle_ko
GSM8560174 muscle_ko 2 muscle_ko
GSM8560175 muscle_ko 3 muscle_ko
GSM8560176 bone_con 1 bone_con
GSM8560177 bone_con 2 bone_con
GSM8560178 bone_con 3 bone_con
GSM8560179 bone_ko 1 bone_ko
GSM8560180 bone_ko 2 bone_ko
GSM8560181 bone_ko 3 bone_ko

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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.