GEO series
Central amygdala single-nucleus atlas reveals chromatin and gene transcription dynamics in human alcohol use disorder
GSE336954
Homo sapiens; Mus musculus
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
126 samples
Submitted 2026/07/01
Platform GPL24676Platform GPL24247
Summary
Regulation of gene expression is a highly coordinated process in both the healthy and pathological brain with unique patterns across a multitude of cell types. Here we present a multi-omic single nucleus study of ~175,000 nuclei from 50 donors with alcohol use disorder (AUD) and control donors without AUD, profiling cell type specific gene expression and chromatin accessibility in the human central amygdala. We identify all major CNS cell types and neuronal subtypes and find inhibitory neurons are particularly affected by AUD. We find high numbers of differentially expressed genes (DEGs) including GABRA2, GRM8, and NCAM1 and show significant enrichment for AUD risk genes within these DEGs. We identified 51,431 cell type-specific, disease associated candidate cis-regulatory elements including an interneuron-associated set of chromatin loops at the AUD risk gene CALN1. Transcription factor footprinting identified Kruppel-like factors upstream of AUD GWAS genes and DEGs. Finally, we also perform cell type-specific fine mapping for AUD GWAS to prioritize variants within functional genomic elements.
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE336954_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 126 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1483640 and SRA study SRP713623. Searching any of these in the dataset finder brings you back here.
Study design
40 conditions, each sampled once — no replicated groups
Read from the first 40 of 126 sample titles: 40 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
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- GSM9845202 Multiome, central amygdala, RT00254N, CON, human, GEX
- GSM9845203 Multiome, central amygdala, RT00254N, CON, human, ATAC
- GSM9845204 Multiome, central amygdala, RT00255N, AUD, human, GEX
- GSM9845205 Multiome, central amygdala, RT00255N, AUD, human, ATAC
- GSM9845206 Multiome, central amygdala, RT00256N, CON, human, GEX
- GSM9845207 Multiome, central amygdala, RT00256N, CON, human, ATAC
- GSM9845208 Multiome, central amygdala, RT00257N, CON, human, GEX
- GSM9845209 Multiome, central amygdala, RT00257N, CON, human, ATAC
- GSM9845210 Multiome, central amygdala, RT00258N, CON, human, GEX
- GSM9845211 Multiome, central amygdala, RT00258N, CON, human, ATAC
- GSM9845212 Multiome, central amygdala, RT00259N, AUD, human, GEX
- GSM9845213 Multiome, central amygdala, RT00259N, AUD, human, ATAC
- GSM9845214 Multiome, central amygdala, RT00260N, CON, human, GEX
- GSM9845215 Multiome, central amygdala, RT00260N, CON, human, ATAC
- GSM9845216 Multiome, central amygdala, RT00261NRP, CON, human, GEX
- GSM9845217 Multiome, central amygdala, RT00261NRP, CON, human, ATAC
- GSM9845218 Multiome, central amygdala, RT00262N, AUD, human, GEX
- GSM9845219 Multiome, central amygdala, RT00262N, AUD, human, ATAC
- GSM9845220 Multiome, central amygdala, RT00263N, AUD, human, GEX
- GSM9845221 Multiome, central amygdala, RT00263N, AUD, human, ATAC
- GSM9845222 Multiome, central amygdala, RT00264N, CON, human, GEX
- GSM9845223 Multiome, central amygdala, RT00264N, CON, human, ATAC
- GSM9845224 Multiome, central amygdala, RT00265NRP, CON, human, GEX
- GSM9845225 Multiome, central amygdala, RT00265NRP, CON, human, ATAC
- GSM9845226 Multiome, central amygdala, RT00269N, AUD, human, GEX
- GSM9845227 Multiome, central amygdala, RT00269N, AUD, human, ATAC
- GSM9845228 Multiome, central amygdala, RT00270N, AUD, human, GEX
- GSM9845229 Multiome, central amygdala, RT00270N, AUD, human, ATAC
- GSM9845230 Multiome, central amygdala, RT00271N, CON, human, GEX
- GSM9845231 Multiome, central amygdala, RT00271N, CON, human, ATAC
- GSM9845232 Multiome, central amygdala, RT00273N, AUD, human, GEX
- GSM9845233 Multiome, central amygdala, RT00273N, AUD, human, ATAC
- GSM9845234 Multiome, central amygdala, RT00274N, AUD, human, GEX
- GSM9845235 Multiome, central amygdala, RT00274N, AUD, human, ATAC
- GSM9845236 Multiome, central amygdala, RT00275N, AUD, human, GEX
- GSM9845237 Multiome, central amygdala, RT00275N, AUD, human, ATAC
- GSM9845238 Multiome, central amygdala, RT00276N, CON, human, GEX
- GSM9845239 Multiome, central amygdala, RT00276N, CON, human, ATAC
- GSM9845240 Multiome, central amygdala, RT00277N, CON, human, GEX
- GSM9845241 Multiome, central amygdala, RT00277N, CON, human, ATAC
+ 86 more — browse all 126 samples with per-sample file links →
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