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ACSS2 plays a role in mediating lasting transcriptomic dysregulation in the dorsal hippocampus and cerebellar vermis of mice chronically prenatally exposed to alcohol

GSE310211 Mus musculus (mouse) RNA-seq (gene expression) 32 samples Submitted 2026/03/09 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 32 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
32 samples: 16 conditions, mostly in duplicateGroups 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
ACSS2 mediates prenatal alcohol exposure-related morphological and behavioral phenotypesNeurobiology of disease · 2026
Summary (written by the submitters)
BACKGROUND: Recent findings showed that alcohol-derived acetate contributes to ACSS2-dependent histone acetylation in the brain, and this metabolic-epigenetic mechanism regulates alcohol-associated learning. Further, alcohol-derived acetate is incorporated into histone acetylation in gestating fetal brains following acute maternal alcohol exposure in late pregnancy (E18.5).
Read the full summary ↓
GOAL: Determine any role of ACSS2 in mediating chronic prenatal alcohol exposure (cPAE)-driven lasting transcriptomic effects in the brain. APPROACH: We used RNA sequencing to investigate the lasting cPAE-related transcriptomic effects in the dorsal hippocampus (dHPC) and cerebellar vermis of adolescent WT and ACSS2 KO mice. These two brain regions were selected because of their implications in hallmark FASD phenotypes (long-term memory impairments and motor deficits, respectively). The chronic prenatal exposure model was a daily i.p. injection (3 g/kg ethanol or equivalent volume saline) to pregnant dams from E0.5 until pups were born. FINDINGS: cPAE resulted in lasting gene and transcript expression changes in both of these brain regions of both genotypes compared to respective saline (cPSE)-treated controls. There were few enriched biological processes, indicating cPAE has widespread lasting transcriptomic effects across a variety of pathways. cPAE-related differentially expressed features (DEFs: DEGs and DETs) were nearly entirely specific to genotype, evidenced by very few DEFs overlapping between genotypes. All but one of these overlapping DEFs were oppositely affected between genotypes. Further, there were hundreds of DEFs exhibiting significant interaction between genotype and prenatal exposure. Taken together, these findings suggest that lasting cPAE-related transcriptomic dysregulation is in part modulated by ACSS2.
Published in
ACSS2 mediates prenatal alcohol exposure-related morphological and behavioral phenotypes
Dodson KM, Periandri EM, Yadav A et al. · Neurobiology of disease 2026 · PMID 41780700 · doi:10.1016/j.nbd.2026.107341
This dataset
Open GSE310211 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 GSE310211_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 PRJNA1365307 and SRA study SRP645531. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41780700) ↗
Study design
16 conditions, mostly in duplicate
RNA_WT_cPSE_dHPC-M ×2 RNA_WT_cPSE_dHPC-F ×2 RNA_WT_cPAE_dHPC-M ×2 RNA_WT_cPAE_dHPC-F ×2 RNA_KO_cPSE_dHPC-M ×2 RNA_KO_cPSE_dHPC-F ×2 RNA_KO_cPAE_dHPC-M ×2 RNA_KO_cPAE_dHPC-F ×2 +8 more

Supports a between-group comparison across 32 samples.

How we read this: 16 replicated groups read from 32 sample titles; they account for 32 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
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