Genome-wide RNA-Seq analysis of mRNA in ipsilateral and contralateral hemispheres of the rat brain at 24 h after tMCAO

White 2-month-old male rats of the Wistar line (weight, 200-250 g) were used. The model of transient cerebral focal ischemia (tMCAO) was used. The animals were divided into the "sham-operation" (SH), and "tMCAO" (IR24) groups. Each group contained 3 animals. tMCAO in experimental rats was initiated by endovascular occlusion of right middle cerebral artery using monofilament for 90 minutes followed by reperfusion. The anaesthesia was induced by 3% isoflurane and maintained by 1.5-2% isoflurane. Anesthesia was used only for the filament insertion and removal, while in between these procedures the rats were taken out of anesthesia. The sham-operated rats were subjected to a similar surgical procedure under anaesthesia (neck incision and separation of the bifurcation), but without tMCAO. At 24 h after sham/tMCAO operation, rats were decapitated. In rats subjected to tMCAO, the subcortical structures of the brain were isolated from the ipsilateral hemisphere (IH) ("IR-i" group of samples) and from the contralateral hemisphere (CH) ("IR-c" group of samples). From the brain of sham-operated rats, subcortical regions were isolated from the right hemisphere, corresponding to the IH of is-chemic rats ("SH-i" group of samples), and from the left hemisphere, corresponding to the CH of ischemic animals ("SH-c" group of samples). All samples obtained from IR-i, IR-c, SH-i, and SH-c were placed in RNAlater. The mRNA fraction was subjected to High-throughput RNA-sequencing (RNA-Seq). Sequencing was done using an Illumina HiSeq 1500 instrument. At least 10 million reads (1/50 nt) were generated.