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Benefits of Maternal choline supplementation on aged basal forebrain cholinergic neurons in a mouse model of Down syndrome and Alzheimer’s disease

GSE296095 Mus musculus (mouse) RNA-seq (gene expression) 44 samples Submitted 2025/08/05 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 44 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
44 samples: 44 samples, each with a distinct title — no replicated groupsGroups 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)
Down syndrome (DS) stemming from triplication of chromosome 21 causes intellectual disability, with early onset of Alzheimer’s disease (AD) pathology in mid-life. Early intervention studies to reduce cognitive impairments and onset of pathology are lacking. One such treatment, maternal choline supplementation (MCS), has shown beneficial effects on behavior and gene expression in neurodegenerative and neurodevelopmental diseases in rodent models including DS mouse models.
Read the full summary ↓
Basal forebrain cholinergic neuron (BFCN) degeneration and enlarged endosomal phenotype is reduced due to maternal choline supplementation (MCS) in a mouse model of Down Syndrome (Ts65Dn) with concomitant beneficial behavioral effects. However, the underlying mechanisms and gene expression alterations during aging and BFCN degeneration are understudied. We postulate cellular mechanisms driving these alterations will be elucidated with novel therapeutic targets identified by examining the modulation in MCS treated aged DS mice. Immunohistochemical ChAT staining in the medial septal/ventral diagonal band area of the basal forebrain in ~11 MO DS and control (2N) mice with and without MCS was performed. Approximately 500 cholinergic positive neurons per animal were microisolated for RNA-sequencing. Bioinformatic analysis elucidated gene expression alterations in the aged DS mouse model compared to controls which were attenuated by MCS treatment in the DS and control animals, including cognitive impairment and NAD signaling pathway. In conclusion, MCS treatment shows moderate effects on gene expression in aged BFCNs, indicating that MCS prolongs the healthspan in this DS mouse model, but does not eliminate disease onset.
This dataset
Open GSE296095 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 GSE296095_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 PRJNA1257787 and SRA study SRP582577. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
44 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 44 sample titles: 44 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

+ 4 more — browse all 44 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.