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Pathway-based network medicine identifies novel natural products for Alzheimer's disease

GSE270100 Mus musculus (mouse) RNA-seq (gene expression) 25 samples Submitted 2025/02/19 Platform GPL13112
At a glance

RNA-seq (gene expression) · mouse · 25 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
25 samples: 5 conditions, mostly with about 5 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
Pathway-based network medicine identifies novel natural products for Alzheimer's diseaseAlzheimer's research & therapy · 2025
Summary (written by the submitters)
Natural products exhibit potential as candidates for developing multi-target agents for Alzheimer's disease treatment. The aim of this study is to utilize network-based medicine to identify novel natural products for Alzheimer's disease, and investigate their efficacy and mechanisms of action. In this study, we identified (-)-Vestitol and Salviolone as new potential natural products for treating Alzheimer's disease via an Alzheimer's disease-related pathway-gene network.
Read the full summary ↓
Both natural products improved the cognition of APP/PS1 transgenic mice, reduced Aβ deposition, and lowered soluble toxic Aβ levels in the brain. Notably, a synergistic effect was observed when the two natural products were combined. Transcriptomic analysis and qRT-PCR experiments revealed that the synergistic mechanism of (-)-Vestitol and Salviolone combination is associated with the regulation of a broader range of AD-related pathways and genes, particularly the neuroactive ligand-receptor interaction pathway and calcium signaling pathway.
Published in
Pathway-based network medicine identifies novel natural products for Alzheimer's disease
Liang Y, Xie S, Jia J · Alzheimer's research & therapy 2025 · PMID 39953559 · doi:10.1186/s13195-025-01694-x
This dataset
Open GSE270100 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 GSE270100_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 PRJNA1124993 and SRA study SRP514476. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39953559) ↗
Study design
5 conditions, mostly with about 5 replicates each
Brain cortex, disease model control, n ×5 Brain cortex, (-)-Vestitol, n ×5 Brain cortex, Salviolone, n ×5 Brain cortex, (-)-Vestitol and Salviolone, n ×5 Brain cortex, wild type control, n ×5

Supports a between-group comparison across 25 samples.

How we read this: 5 replicated groups read from 25 sample titles; they account for 25 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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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.