GEO series
Genomic and Behavioral Signatures of Selection for Ethanol Preference from the Heterogeneous Stock Collaborative Cross Mice – The Central Nucleus of the Amygdala
GSE288772
Mus musculus (mouse)
Single-nucleus RNA-seq
200 samples
Submitted 2025/07/23
Platform GPL24247
At a glance
Single-nucleus RNA-seq · mouse · 200 samples
- What it is
- Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Mus musculus (mouse)
- Samples
- 200 samples: 200 × CeA Sample From MouseGroups 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
- Genomic and Behavioral Signatures of Selection for Ethanol Preference from the Heterogeneous Stock Collaborative Cross Mice - The Central Nucleus of the AmygdalaAddiction neuroscience · 2025
Summary (written by the submitters)
Alcohol use disorder (AUD) is a complex disease with heritability of ~0.5, indicating genetic and non-genetic factors contribute to risk. Identifying gene expression networks contributing to risk using post-mortem human brain tissue has the limitation of conflating risk for AUD with consequences of alcohol use. We leveraged mice selectively bred for differential ethanol preference from a highly genetically diverse population to overcome this limitation.
Read the full summary ↓
Ethanol intake was highly correlated with preference, high-preferring (HP) mice consumed more sweet- but not bitter-tasting solutions compared to low-preferring (LP) mice, and the lines did not differ in rate of ethanol elimination. Adult, ethanol-naïve HP and LP mice contributed tissue from the central nucleus of the amygdala (CeA), a region critical to ethanol preference and intake. Single-nuclei and bulk RNA sequencing data were used to identify cell types and transcriptome changes related to selective breeding for differential risk for ethanol preference. Single nuclei analysis identified populations of inhibitory (~48% of cells) and excitatory (~23%) neurons, and non-neuronal (~29%) cells, but no differences in cell-type composition or gene expression were identified between the lines. Bulk CeA analysis identified differences between the lines for: (1) gene expression (2996 genes), (2) expression variability (426 genes), and (3) wiring (407 significant gene-gene correlations). Overall, lower variance was found in the HP line. Reduced gene-gene correlation, also found in HP mice, suggested that selection for high preference induced changes in transcriptional regulation resulting in reduced connectivity, specific to gene networks enriched in markers for inhibitory neurons expressing Isl1 and Tac1.
Published in
Anderson JQ, Darakjian P, Hitzemann R et al.
· Addiction neuroscience 2025
· PMID 40693020
· doi:10.1016/j.addicn.2025.100209
This dataset
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.
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 GSE288772_RAW.tar (it can run to tens of gigabytes).
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.
What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1219228 and SRA study SRP561588. Searching any of these in the dataset finder brings you back here.
Study design
200 × CeA Sample From Mouse
Supports a between-group comparison across 200 samples.
How we read this: 1 replicated groups read from 200 sample titles; they account for 200 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
- GSM8775086 CeA Sample From Mouse 3 CeA Sample From Mouse
- GSM8775087 CeA Sample From Mouse 4 CeA Sample From Mouse
- GSM8775088 CeA Sample From Mouse 7 CeA Sample From Mouse
- GSM8775089 CeA Sample From Mouse 8 CeA Sample From Mouse
- GSM8775090 CeA Sample From Mouse 11 CeA Sample From Mouse
- GSM8775091 CeA Sample From Mouse 12 CeA Sample From Mouse
- GSM8775092 CeA Sample From Mouse 15 CeA Sample From Mouse
- GSM8775093 CeA Sample From Mouse 16 CeA Sample From Mouse
- GSM8775094 CeA Sample From Mouse 19 CeA Sample From Mouse
- GSM8775095 CeA Sample From Mouse 20 CeA Sample From Mouse
- GSM8775096 CeA Sample From Mouse 23 CeA Sample From Mouse
- GSM8775097 CeA Sample From Mouse 24 CeA Sample From Mouse
- GSM8775098 CeA Sample From Mouse 25 CeA Sample From Mouse
- GSM8775099 CeA Sample From Mouse 26 CeA Sample From Mouse
- GSM8775100 CeA Sample From Mouse 27 CeA Sample From Mouse
- GSM8775101 CeA Sample From Mouse 28 CeA Sample From Mouse
- GSM8775102 CeA Sample From Mouse 29 CeA Sample From Mouse
- GSM8775103 CeA Sample From Mouse 30 CeA Sample From Mouse
- GSM8775104 CeA Sample From Mouse 31 CeA Sample From Mouse
- GSM8775105 CeA Sample From Mouse 32 CeA Sample From Mouse
- GSM8775106 CeA Sample From Mouse 33 CeA Sample From Mouse
- GSM8775107 CeA Sample From Mouse 34 CeA Sample From Mouse
- GSM8775108 CeA Sample From Mouse 35 CeA Sample From Mouse
- GSM8775109 CeA Sample From Mouse 36 CeA Sample From Mouse
- GSM8775110 CeA Sample From Mouse 37 CeA Sample From Mouse
- GSM8775111 CeA Sample From Mouse 38 CeA Sample From Mouse
- GSM8775112 CeA Sample From Mouse 39 CeA Sample From Mouse
- GSM8775113 CeA Sample From Mouse 40 CeA Sample From Mouse
- GSM8775114 CeA Sample From Mouse 41 CeA Sample From Mouse
- GSM8775115 CeA Sample From Mouse 42 CeA Sample From Mouse
- GSM8775116 CeA Sample From Mouse 43 CeA Sample From Mouse
- GSM8775117 CeA Sample From Mouse 44 CeA Sample From Mouse
- GSM8775118 CeA Sample From Mouse 45 CeA Sample From Mouse
- GSM8775119 CeA Sample From Mouse 46 CeA Sample From Mouse
- GSM8775120 CeA Sample From Mouse 47 CeA Sample From Mouse
- GSM8775121 CeA Sample From Mouse 48 CeA Sample From Mouse
- GSM8775122 CeA Sample From Mouse 49 CeA Sample From Mouse
- GSM8775123 CeA Sample From Mouse 50 CeA Sample From Mouse
- GSM8775124 CeA Sample From Mouse 51 CeA Sample From Mouse
- GSM8775125 CeA Sample From Mouse 52 CeA Sample From Mouse
+ 160 more — browse all 200 samples with per-sample file links →
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Share this dataset
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.