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Premature aging in growth-plate and periosteum resident skeletal stem cells is responsible for bone loss

GSE182540 Mus musculus (mouse) Single-cell RNA-seq 28 samples Submitted 2024/04/24 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 28 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
28 samples: 8 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.
Paper
Premature aging of skeletal stem/progenitor cells rather than osteoblasts causes bone loss with decreased mechanosensationBone research · 2023
Summary (written by the submitters)
Skeleton system has shown high cell heterogeneousity. Different subpopulation of skeleton stem cells or mesenchymal stem cells have been identified by using varied protein markers. However, the decline of which cell types are responsible for age-related bone loss and what characteristic changes of these cells during aging remain to be determined.
Read the full summary ↓
In the current study, we constructed a conditional premature aging model by deletion of Zmpste24 (Z24) in different cell types. We found that Prx1Cre; Z24fl/fl mice displayed bone loss while OsxCre; Z24fl/fl mice did not, indicating the populations of Prx1Cre +Osxcre- cells are responsible for age-related bone loss. Using single-cell RNA sequencing, we found two populations exit in Prx1Cre; Ai9+ mice but not in OsxCre; Ai9+ mice. Most strikingly, these two populations were declined in Prx1Cre;Z24fl/fl mice, compared to Prx1Cre;Z24fl/+ mice. The two populations, one is Prx1Cre;CD73+ resident in growth plate, called gpSSCs, responsible for trabecular bone loss. Another is Prx1Cre; Sca1+ resident in periosteum, called pSSCs, responsible cortical bone decrease. More importantly, the naturally aged mice also showed the decrease of these two cell types. By integration of chromatin and transcriptional profiling, we found that these two cell populations displayed increased p53 mediated DNA damage and decreased extracellular matrix (ECM) constituents, supporting the degeneration of two populations during aging. Finally, we found that AgrcCreER Z24fl/fl mice displayed the decrease of trabecular bone, but not cortical bone, consistent with AgrcCreER could only label trabecular bone, but not cortical bone. Overall, our study identified two skeleton stem cells, gpSSCs and pSSCs, which are responsible for the age-related bone loss in trabecular bone and cortical bone, respectively.
Published in
Premature aging of skeletal stem/progenitor cells rather than osteoblasts causes bone loss with decreased mechanosensation
Yang R, Cao D, Suo J et al. · Bone research 2023 · PMID 37407584 · doi:10.1038/s41413-023-00269-6
This dataset
Open GSE182540 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 GSE182540_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 PRJNA756693 and SRA study SRP333558. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37407584) ↗
Study design
8 conditions, mostly in triplicate
pSSCs-bulkRNAseq-ctrl ×3 pSSCs-bulkRNAseq-cko ×3 gpSSCs-bulkRNAseq-ctrl ×3 gpSSCs-bulkRNAseq-cko ×3 pSSCs-bulkATACseq-ctrl ×3 pSSCs-bulkATACseq-cko ×3 gpSSCs-bulkATACseq-ctrl ×3 gpSSCs-bulkATACseq-cko ×3 +4 more

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 28 sample titles; they account for 24 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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