GSM9659362: 5C-11; Mus musculus; RNA-Seq
Control and HTRA2 mutant mice were exposed to 21% and 11% oxygen. Starting at postnatal day P11, pups were transferred to the appropriate oxygen condition along with their mother (they were not weaned until ~P21). ~P30, brain was harvested and flash frozen. For striatal microdissection, frozen hemi-brains were kept on dry ice and embedded in a thin layer of 0.6% low-melting-point agarose (Invitrogen Cat #15517-014) prepared in advance and maintained at 37°C. A thin layer of agarose was laid on filter paper placed in the tissue chopper platform, and the frozen hemi-brain was positioned flat on the filter paper. Additional agarose was added on top to fully cover the brain in a hill shape. Once the agarose solidified (~3 minutes), brains were coronally sectioned at 400–500 µm using a McIlwain Tissue Chopper equipped with Stoelting blades (#51352). Sections were transferred into dissection buffer (PBS with protease inhibitors, Roche #05892953001), and the striatum was carefully dissected under a dissection microscope. Dissected tissues were flash-frozen on dry ice and stored at –80°C. Total RNA was isolated from striatum tissue and purified using a Direct-zol RNA MicroPrep Kit (Zymo Research, Cat# R2062) as described by the manufacturer. RNA-seq library preparation was performed according to the manufacturer's instructions of the QuantSeq 3' mRNA-Seq V2 Library Prep Kit (Lexogen Inc, Cat# 193.384