title: GSM3455016: 1009L; Mus musculus; RNA-Seq
library_construction_protocol: After the middle cerebral artery occlusion, animal brains were removed, and the ipsilateral (IPC treatment) and contralateral cortices (serve as control) of the same brain were collected. Total RNA was isolated from three mouse brains using Trizol reagent. A total of two micrograms of RNA per sample was used as input material for library construction. Genomic DNA was isolated from three mouse brains using a DNeasy Blood & Tissue Kit according to the manufacturer's instructions. A total of 500 ng of DNA spiked with 5 ng of lambda DNA (Promega, Madison, WI) per sample was used as input material for library construction. Ribosomal RNA (rRNA) was removed by an Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA) according to the manufacturer's instructions. Subsequently, strand-specific sequencing libraries were generated with the dUTP method using the resulting RNA by an NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer's recommendations. For WGBS, a total of 500 ng of DNA spiked with 5 ng of lambda DNA (Promega, Madison, WI) per sample was fragmented to 250-350 bp by sonication with a Covaris M220, followed by end repair and methylated adaptor ligation. These DNA fragments were treated with bisulfite using an EZ DNA Methylation-Gold TM Kit. The obtained single-strand DNA fragments were amplified by PCR using KAPA HiFi HotStart Uracil + ReadyMix (2x) followed by purification by AMPure XP magnetic beads. The library concentration was quantified by a Qubit 2.0 Fluorometer, and the insert size was assessed on an Agilent Bioanalyzer 2100 system. RNA-Seq, WGBS
attributes.tag: GEO Accession
attributes.value: GSM3455016