GEO series

Gene expression + ATAC profiling of trisomic hippocampal neurons upon SAHA treatment [RNA-seq]

GSE328496 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2026/08/07 Platform GPL17021

At a glance

RNA-seq (gene expression) · mouse · 16 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: 16 samples: 16 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) is associated with widespread molecular alterations, including aberrant gene expression, which not only affects chromosome 21 genes but perturbs the whole transcriptome. The genome-wide nature of this alteration suggests that it might be epigenetically mediated, which may also offer therapeutic opportunities given the reversibility of epigenetic modifications.

Read the full summary ↓

Here, we show that decreased global acetylation level in the hippocampus of the trisomic mouse model Ts65Dn is associated with decreased chromatin accessibility at gene promoters in hippocampal neurons. Strikingly, pharmacological restoration of histone acetylation using the clinically approved histone deacetylase inhibitor suberoylanilide hydroxamic acid (SAHA) normalized transcriptomic, epigenetic and cortico-hippocampal memory deficits in trisomic mice. This rescue was mediated by an unexpected heterochromatization of the supernumerary chromosome. Altogether, our results identify an unanticipated epigenetic mechanism linking histone acetylation dynamics to chromosomal dosage homeostasis.

This dataset

Open GSE328496 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 GSE328496_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 PRJNA1455548 and SRA study SRP693172. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

16 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 16 sample titles: 16 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

GSM9684423 WT naive Hippocampal neurons, replicate 1, RNA-seq
GSM9684424 WT naive Hippocampal neurons, replicate 2, RNA-seq
GSM9684425 TS naive Hippocampal neurons, replicate 1, RNA-seq
GSM9684426 TS naive Hippocampal neurons, replicate 2, RNA-seq
GSM9684427 TS naive Hippocampal neurons, replicate 3, RNA-seq
GSM9684428 WT NOR Hippocampal neurons, replicate 1, RNA-seq
GSM9684429 WT NOR Hippocampal neurons, replicate 2, RNA-seq
GSM9684430 WT NOR Hippocampal neurons, replicate 3, RNA-seq
GSM9684431 WT NOR Hippocampal neurons, replicate 4, RNA-seq
GSM9684432 TS NOR Hippocampal neurons, replicate 1, RNA-seq
GSM9684433 TS NOR Hippocampal neurons, replicate 2, RNA-seq
GSM9684434 TS NOR Hippocampal neurons, replicate 3, RNA-seq
GSM9684435 TS NOR Hippocampal neurons, replicate 4, RNA-seq
GSM9684436 TS+SAHA NOR Hippocampal neurons, replicate 1, RNA-seq
GSM9684437 TS+SAHA NOR Hippocampal neurons, replicate 2, RNA-seq
GSM9684438 TS+SAHA NOR Hippocampal neurons, replicate 3, RNA-seq

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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.