GSM3288309: D2420-Y-APOE3het-M-T; Mus musculus; RNA-Seq
Fourteen days post-injury, mice were anesthetized using Avertin (250 mg/kg of body weight, i.p.) and perfused transcardially with 20mL of cold 0.1M PBS pH 7.4. Brains were rapidly removed and a 1.5 mm coronal section of the brain, including the injury site, taken by slicing the brain at -2.5 mm and -4.0 mm from bregma. Within the coronal slice, the hemispheres were separated, and the subcortical tissue was dissected out; hippocampal and cortical tissue were snap-frozen together for RNA isolation and RNA-seq. RNA was isolated from frozen cortices and hippocampi at the injury site and purified using RNeasy kit (Qiagen) according to the manufacturer recommendations. Quality control of all RNA samples was performed on a 2100 Bioanalyzer instrument (Agilent Technologies) and samples with RIN > 8 were further used for library construction. Quality control of all RNA samples was performed on a 2100 Bioanalyzer instrument (Agilent Technologies) and samples with RIN > 8 were further used for library construction using RNA Library Prep Reagent Set (Illumina). Libraries for Next Generation Sequencing were generated by PCR enrichment including incorporation of barcodes to enable multiplexing. Sequencing was performed by the Next Generation Sequencing Center (University of Pennsylvania, http://fgc.genomics.upenn.edu/) on HiSeq 2500 machine.