Pluto Bioinformatics

GSE83498: Profiling the transcriptome of murine radial glial and astrocyte precursor cells

Bulk RNA sequencing

The goal of this study is to evaluate transcriptome profiles that accompany mouse radial glial cells and astrocytes isolated from the developing central nervous system.; GLAST-positivity, a marker of radial glia and astrocyte lineage, was exploited to isolate cells from postnatal day 0 (P0) and P8 mouse brains using GLAST-specific antibodies conjugated to magnetic beads. mRNA from four separate biological replicates of GLAST-positive cells for each postnatal stage were used to construct cDNA libraries following TruSeq RNA sample preparation. Sequencing of libraries was conducted on Illumina HiSeq2000 using 100bp paired-end reads with 25 million reads per sample. Sequenced reads were aligned to the mouse genome (mm9) with the TopHat workflow and fragments per kilobase of transcript per million (FPKM) was calculated. Differential expression was determined using EdgeR with continuous dispersion and false discovery rate was calculated.; RNA-seq data confirmed appropriate expression of 45 known housekeeping genes from different cell types in both P0 and P8 post-natal mouse brain. Differential expression of 1438 genes at P0 and 1100 at P8 GLAST-positive cells were found to have a fold change 2 and FDR <0.05. 18 genes were confirmed with qRT-PCR, demonstrating the validity of the RNA-seq method. SOURCE: Jonathan,Matthew,Wilson (wilsonjo@lilly.com) - SL362 IUPUI