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Senescent cell elimination modifies features of Alzheimer’s disease in 3xTg-AD mice

GSE231332 Mus musculus (mouse) RNA-seq (gene expression) 28 samples Submitted 2024/03/20 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 28 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
28 samples: 7 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
Senescence Targeting Methods Impact Alzheimer's Disease Features in 3xTg MiceJournal of Alzheimer's disease : JAD · 2024
Summary (written by the submitters)
Cellular senescence has been associated with neurodegenerative disease and clearance of senescent cells using genetic or pharmaceutical strategies (senolytics) has demonstrated beneficial effects in mouse models investigating individual disease etiologies of Alzheimer’s disease (AD). However, it has remained unclear if senescent cell clearance in a mouse model exhibiting both plaque and tau pathologies modifies the disease state (3xTg).
Read the full summary ↓
Here, we show that treatment with senolytics (ABT263 (navitoclax) or a combination of dasatinib and quercetin (D+Q)) or transgenic removal of p16-expressing cells (via INK-ATTAC) reduced microgliosis and ameliorated both amyloid and tau pathology in 3xTg mice. Using RNA sequencing, we found evidence that synaptic dysfunction and neuroinflammation was attenuated with senescent cell removal. Unfortunately, these beneficial effects were not seen with short-term senolytic treatment in mice with more advanced disease. Overall, our results further corroborate the beneficial effects senescent cell clearance could have on AD and highlight the importance of early intervention for treatment of this debilitating disease.
Published in
Senescence Targeting Methods Impact Alzheimer's Disease Features in 3xTg Mice
Ng PY, Zhang C, Li H et al. · Journal of Alzheimer's disease : JAD 2024 · PMID 38306030 · doi:10.3233/JAD-230465
This dataset
Open GSE231332 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 GSE231332_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 PRJNA963864 and SRA study SRP435229. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38306030) ↗
Study design
7 conditions, mostly with about 4 replicates each
Hippocampus, 3xTg, DQ treated, ×4 Hippocampus, 3xTg, NAVI treated, ×4 Hippocampus, 3xTg, VehN treated, ×4 Hippocampus, 3xTg, VehD treated, ×4 Hippocampus, BL6129, DQ treated, ×4 Hippocampus, BL6129, NAVI treated, ×4 Hippocampus, BL6129, Veh treated, ×4

Supports a between-group comparison across 28 samples.

How we read this: 7 replicated groups read from 28 sample titles; they account for 28 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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