RNA sequencing in Prnp^WT/WT , Prnp^ZH1/ZH1 , and Prnp^ZH3/ZH3 hippocampi. RNA sequencing was performed on hippocampi from four mice per each group. (A) Physical distribution of sequence variant density across the genome based on variants unique to Prnp^ZH1/ZH1 (ZH1, left) or Prnp^ZH3/ZH3 (ZH3, right) compared with C57BL/6J mice (BL6). Each dot denotes the ratio of variants and total number of annotated bases in 50-kb windows throughout the genome. Pie charts depict the number (n, proportional to the area) and chromosomal distribution (yellow, chromosome 2; gray, other chromosomes) of sequence variants in the two comparisons. For variant identification, the three mice with the highest coverage within each group were considered. (B) Physical distribution of differential gene expression levels across the genome based on the comparison of Prnp^ZH1/ZH1 (left) or Prnp^ZH3/ZH3 (right) with respect to C57BL/6J mice. Each dot denotes a gene. Pie charts depict the number (n, proportional to the area) and chromosomal distribution (yellow, chromosome 2; gray, other chromosomes) of DEGs (fdr < 0.05 and absolute log2 ratio > 0.5) in the two comparisons.