GSM5769423: IVHControl1; Rattus norvegicus; RNA-Seq
Immediately following transcardial perfusion with ice cold TBS (pH = 7.60), the brain was isolated and placed in an ice-cold saline bath. Brains were cut sagittally along the interhemispheric line to expose the lateral ventricles, and choroid plexuses were rapidly but carefully dissected from both lateral ventricles using sharp forceps under magnification. Each brain yielded ~3 mg of choroid plexus tissue total, which was collected into a 1.5 mL tube, snap frozen in liquid nitrogen, and stored at -80oC until use. Full length high quality total cell RNA isolated by Qiagen RNAeasy micro kit (Quigen, https://www.qiagen.com/us/shop/pcr/rneasy-micro-kit/). ChP cells were homogenized in 350ul RLT buffer with beta-mercaptoethanol in Tissuelyzer for 10 mins and proceed according to the instructions in RNAeasy Micro RNA kit and RNAs was eluted in 18ul dH2O. 16ul of elutant was recovered and 1.2ul was used for the QC. Libraries were run on an Illumina HiSeq 2500 at the Yale Center for Genome Analysis. The R/Bioconductor package “DESeq2” was used to identify differentially expressed genes between cell populations derived from control, IVH-treated and LPS-treated rats (Love et al., 2014). Genes with a log2-fold change expression greater than 3 and a q-value less than 0.01 were considered significant. The R ComplexHeatmap package was used to visualize the heatmap expression of highly variable genes (Gu et al., 2016). Volcano plots were generated using the R package EnhancedVolcano (Blighe et al., 2019).