RNAseq after cortical spreading depolarization (SD)

The present study aimed to perform an extensive, unbiased RNA sequencing (RNA-seq) analysis to identify biological pathways, as well as related diseases and functions, modified by SD in healthy brains. SDs were induced repetitively (2 hours, 30 min intervals) in healthy, female mice and monitored with intrinsic optical signal (IOS) imaging. SD induction was with either focal application of KCl in C57Bl/6 mice or with optogenetic stimulation in Thy1-ChR2-YFP mice. Two hours after onset of SD, total cortical RNA was extracted and subjected to Illumina paired-end RNA sequencing to identify differentially expressed genes (DEGs; fold change >1.25, p-value <0.05). We identified 101 significantly upregulated genes after KCl-induced SDs and 136 after optogenetic induction; of these 57 (31.7%) genes were in common. Overall design: SDs were induced repetitively (4 SDs in 2 hours at 30 min intervals) in healthy, 7- to 8-week-old female mice and SDs were confirmed with intrinsic optical signal imaging. SD induction was with either focal application of KCl (NaCl for sham controls, n=6) in C57Bl/6 mice or with optogenetic stimulation (2 mW for 20 seconds) in Thy1-ChR2-YFP heterozygous mice (n=6).