ATAC-seq of mouse cortex undergoing early degradation after traumatic brain injury (TBI)

Advances in molecular diagnostics have enabled accurate disease diagnosis. However, the application of molecular biology technology in the field of forensic medicine, especially in forensic pathology, is still limited. Degraded samples with altered physicochemical properties pose challenges for molecular techniques. Identifying degradation-resistant, sensitive techniques is key for forensic molecular pathology. ATAC-seq maps open chromatin and is increasingly used in disease diagnosis and mechanism studies. Given forensic use of degraded DNA, we explored ATAC-seq's potential for analyzing degraded forensic samples. In a TBI model, ATAC-seq detected injury-induced chromatin changes after 2h degradation. We identified 1,432 TBI-associated loci with robust chromatin changes unaffected by degradation. These loci have potential as a panel of biomarkers for molecular diagnosis from degraded forensic samples. Overall design: The mice were randomly divided into four groups: Sham_0H, Sham_2H, TBI_0H, and TBI_2H, with three mice in each group.Mice were subjected to a controlled cortical impact (CCI) procedure with craniotomy.Two hours post-operation, the mice were anesthetized and underwent transcardial perfusion with 10ml of isotonic saline. The mice were randomly divided into four groups: Sham_0H, Sham_2H, TBI_0H, and TBI_2H, with three mice in each group.Sham mice did not undergo impact, but all other procedures were the same as those for the TBI mice. Tissue collection was performed 2 hours post-mortem for the Sham_2H and TBI_2H groups, while for the Sham_0H and TBI_0H groups, tissue collection was done immediately after euthanasia.