Multi-omic Enhancer–Promoter Links from Striatal snATAC-/snRNA-seq Across Eight Genetically Diverse Mouse Strains
Year: 2024
Type: dataset
Abstract: DescriptionThis dataset contains enhancer–promoter links inferred from a multi-omic snATAC-seq/snRNA-seq dataset generated from the striatum of eight genetically diverse inbred mouse strains representing the founder strains of the Diversity Outbred (DO) and Collaborative Cross (CC) populations. The dataset includes striatopallidal Drd1 and Drd2 neurons and was analyzed using Enhlink to identify putative regulatory interactions between accessible chromatin regions and target genes.MethodsEnhlink analyses were performed independently using:snATAC-seq data alone;Joint snATAC-seq and snRNA-seq analyses, where chromatin accessibility was correlated with gene expression profiles.For each modality, two analysis strategies were applied:A combined analysis, where Drd1 and Drd2 neurons were pooled together to maximize statistical power for enhancer–promoter link discovery.A Drd1/Drd2 comparative analysis, where neuronal subtype identity (Drd1 versus Drd2) was included as a covariate to identify subtype-associated regulatory interactions.Regulatory links identified from chromatin accessibility and gene expression analyses were subsequently compared to identify interactions supported across modalities.File DescriptionEach BEDPE file contains predicted enhancer–promoter interactions. The first six columns define the genomic coordinates of the linked regions:Columns 1–3: enhancer coordinates (chromosome, start, end)Columns 4–6: promoter coordinates (chromosome, start, end)Additional columns contain Enhlink association statistics for each predicted regulatory interaction.File name suffixes:drd: Drd1/Drd2 comparative analysis in which neuronal subtype identity was incorporated into the model to identify subtype-associated regulatory interactions.Files without the drd suffix correspond to the combined analysis, where Drd1 and Drd2 neurons were pooled prior to enhancer–promoter link inference.SoftwareEnhlinkTools: https://gitlab.com/Grouumf/enhlinktoolsCitationPoirion OB, et al. Enhlink: inferring enhancer–gene regulatory interactions from single-cell chromatin accessibility data. Genome Biology, 2024.
Source: Figshare
Authors: Poirion, Olivier, zuo, wulin, Spruce, Catrina, Daigle, Sandy, Wilson-Smith, Ashley, Skelly, Daniel A., Baker, Christopher, white, brian
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W6977652389