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Allele-resolved liver transcriptomes of CC032 x CC072 F1 mice quantified against a Collaborative Cross founder pantranscriptome

ABSTRACT: RNA-seq on liver tissue from the same two 25-day-old CC032 x CC072 F1 hybrid mice profiled by ATAC-seq in GSE345488 (F19 and F20). Reads were aligned to a spliced Collaborative Cross founder pangenome, which represents each Ensembl transcript by the distinct sequences it takes across the founders, and quantified in a haplotype-aware manner: at each gene the most likely founder-haplotype pair is inferred from read compatibilities, and abundance is then estimated for each haplotype-specific transcript of that pair. The data accompany the allele-specific chromatin accessibility analysis and allow accessibility and expression to be compared haplotype by haplotype in the same animals.

ORGANISM(S): Mus musculus

PROVIDER: GSE346710 | GEO | 2026/09/16

REPOSITORIES: GEO

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Project description:The collaborative cross (CC) founder strains include five classical inbred laboratory strains (129S1/SvlmJ, A/J, C57BL/6J (B6), NOD/ShiLtJ, and NZO/HILtJ) and three wild-derived strains (CAST/EiJ, PWK/PhJ (PWK) and WSB/EiJ) The strains encompass 89% of the genetic diversity available in Mus musculus and about 10 to 20 times more genetic diversity than found in Homo sapiens. For more than 60 years the B6 strain has been used as the model strain for high ethanol preference/high consumption. However, another one of the CC founder strains, PWK, was identified as a high ethanol preference/high consumption strain. The current study determined how the transcriptomes of the B6 and PWK strains differed from the 6 low preference CC strains across 3 nodes of the brain addiction circuit. RNA-Seq data were collected from the central nucleus of the amygdala, the nucleus accumbens core and the prelimbic cortex. Differential expression (DE) analysis was performed in each of these brain regions for all 28 possible pairwise comparisons of the CC founder strains. Unique genes for each strain were identified by selecting for genes that differed significantly (false discovery rate (FDR) < 0.05) from all other strains in the same direction. B6 was identified as the most distinct inbred laboratory strain, having the highest number of total differently expressed genes (DEGs) and DEGs with high log fold change, and unique genes compared to other CC strains. Less than 50 unique DEGs were identified in common between B6 and PWK within all three brain regions, indicating the strains potentially represent two distinct genetic signatures for risk for high ethanol-preference. 238 DEGs were found to be commonly different between B6, PWK and the average expression of the remaining CC strains within all three regions. The commonly different up-expressed genes were significantly enriched (FDR < 0.001) among genes associated with neuroimmune function. These data compliment the observation that neuroimmune signaling is key to understanding alcohol use disorder and and support use of these 8 strains and the highly heterogeneous mouse populations derived from them to identify alcohol-related brain mechanisms and treatment targets.

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Allele-resolved liver transcriptomes of CC032 x CC072 F1 mice quantified against a Collaborative Cross founder pantranscriptome

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