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Diminished transcriptional activity and splicing changes drive gene length-biased rewiring in the aging transcriptome (RNA-Seq)

GSE282096 Mus musculus (mouse) RNA-seq (gene expression) 94 samples Submitted 2026/05/31 Platform GPL24247Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 94 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
94 samples: 30 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
Diminished transcriptional activity and splicing changes drive gene length-biased rewiring in the aging transcriptomeProceedings of the National Academy of Sciences of the United States of America · 2026
Summary (written by the submitters)
Transcription by RNA polymerase II (RNAPII), which is essential for protein-coding gene expression and cellular function, is increasingly understood to become dysregulated with aging. Here, we use a multi-modal approach to comprehensively characterize age-dependent changes in RNAPII-mediated transcription in both mouse and human tissues.
Read the full summary ↓
Short-read total RNA sequencing (RNA-seq) to profile nascent transcription reveals a global reduction in overall transcriptional activity/frequency in aged tissues, without apparent change in elongation rates. Transcriptomic analysis reveals a shift toward preferential expression of short genes in aged tissues, with notable upregulation of short stress-response genes and downregulation of long neurodevelopmental genes in the aged mouse brain. These results are recapitulated by analysis of total RNA-seq data from human tissues. Leveraging long-read RNA-seq, we determine that the representation of aberrant mono-exonic and intron-retention splice isoforms is increased in the aged mouse brain. Finally, we characterize the composition of RNAPII transcriptional machinery, finding that interactions between RNAPII and the Mediator complex are decreased in the chromatin of aged mouse liver and brain. Collectively, these analyses provide insight for future aging studies and reveal potential transcriptional control targets for anti-aging drug development.
Published in
Diminished transcriptional activity and splicing changes drive gene length-biased rewiring in the aging transcriptome
Parast S, Das M, He Y et al. · Proceedings of the National Academy of Sciences of the United States of America 2026 · PMID 42301777 · doi:10.1073/pnas.2607264123
This dataset
Open GSE282096 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 GSE282096_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 PRJNA1187184 and SRA study SRP545673. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42301777) ↗
Study design
30 conditions, mostly in triplicate
RNA_Kidney_O2 ×4 RNA_Kidney_Y2 ×4 RNA_Liver_O1 ×4 RNA_Liver_O2 ×4 RNA_Liver_Y1 ×4 RNA_Liver_Y2 ×4 RNA_Brain_O2 ×3 RNA_Brain_O3 ×3 +22 more

Supports a between-group comparison across 94 samples.

How we read this: 30 replicated groups read from 94 sample titles; they account for 94 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

+ 54 more — browse all 94 samples with per-sample file links →

Datasets on a similar topic

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