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

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.