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Transcriptomic analysis of whole mouse tibia samples

GSE262441 Mus musculus (mouse) RNA-seq (gene expression) 48 samples Submitted 2024/05/23 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 48 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
48 samples: 12 conditions, mostly with about 4 replicates eachGroups 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
Caloric restriction reduces trabecular bone loss during aging and improves bone marrow adipocyte endocrine function in male miceFrontiers in endocrinology · 2024
Summary (written by the submitters)
The combined effects of aging and a dietary intervention of reduced energy intake, caloric restriction, were examined by conducting a bulk transcriptomic analysis of mouse whole tibia bone samples. Tissue samples were collected from mice at two different age groups, comparing old and young animals, with caloric restriction in comparison to full food access.
Published in
Caloric restriction reduces trabecular bone loss during aging and improves bone marrow adipocyte endocrine function in male mice
Rinne C, Soultoukis GA, Oveisi M et al. · Frontiers in endocrinology 2024 · PMID 38904042 · doi:10.3389/fendo.2024.1394263
This dataset
Open GSE262441 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 GSE262441_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 PRJNA1091799 and SRA study SRP497797. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38904042) ↗
Study design
12 conditions, mostly with about 4 replicates each
bone_Y_CR1_tech ×4 bone_Y-Ctrl1-CR-9__tech ×4 bone_Y-CR-2_tech ×4 bone_Y-Ctrl1-CR-10_tech ×4 bone_Y-CR-3_tech ×4 bone_Y-Ctrl1-CR-11_tech ×4 bone_O-CR-5_tech ×4 bone_O-Ctrl1-CR-13_tech ×4 +4 more

Supports a between-group comparison across 48 samples.

How we read this: 12 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 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.