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Bioenergetic programs of cancellous and cortical bone are distinct and differ with age and mechanical loading

GSE281942 Mus musculus (mouse) RNA-seq (gene expression) 150 samples Submitted 2024/11/15 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 150 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
150 samples: 96 distinct titles, 18 of them repeatedGroups 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)
Mechanical loading induces bone formation in young rodents, but mechanoresponsiveness is reduced with age. Glycolytic activity and mitochondrial dysfunction increase with age and may change bone mechanotransduction. To evaluate load-induced changes to bioenergetic activity in young and adult animals, we loaded the tibia of 10-wk and 26-wk female mice and examined transcriptomic responses at the mid-diaphysis, metaphyseal cortical shell, and cancellous core.
Read the full summary ↓
Across all biological processes, oxidative phosphorylation and mitochondrial pathways were most often enriched with loading and had opposite enrichment in young and adult animals. Following loading, young animals had temporally-coordinated differential expression of mitochondrial-associated genes, with greatest expression at the mid-diaphysis. In adults, bioenergetic gene expression was lower compared to young animals.
This dataset
Open GSE281942 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 GSE281942_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 PRJNA1186219 and SRA study SRP545301. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
96 distinct titles, 18 of them repeated
26wk_Cancellous_Loaded Limb _3h _Animal3h ×5 26wk_Metaphyseal Shell_Loaded Limb _3h _Anima… ×5 26wk_Mid-Diaphysis_Loaded Limb _3h _Animal3h ×5 26wk_Cancellous_Contralateral Control Limb _3… ×5 26wk_Metaphyseal Shell_Contralateral Control … ×5 26wk_Mid-Diaphysis_Contralateral Control Limb… ×5 26wk_Cancellous_Loaded Limb _24h _Animal24hO ×4 26wk_Metaphyseal Shell_Loaded Limb _24h _Anim… ×4 +10 more

How we read this: Read from 150 sample titles: 96 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

+ 110 more — browse all 150 samples with per-sample file links →

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.