CNS Conditioning Effect

This dataset look at the CNS conditioning response. Spinal cord lesions were performed 24hrs before neuron isolation from the cortex. Cells were then cultured for 1 day, 2 days, 3 days, 5 days or 7 days in culture. Naive cultures consists of neurons isolated from the cortex with no prior conditioning lesion. Control cells were cultured for 1 day, 2 days, 3 days, 5 days or 7 days in culture. RNA was then isolated and processed for RNA sequencing.
The alignment summary and subsequent differential expression analysis of RNA-seq data collected from a total of 29 mouse samples. Reads were aligned to the latest mouse mm10 reference genome using the STAR spliced read aligner. Total counts of read-fragments aligned to known gene regions within the mouse mm10 refSeq reference annotation are used as the basis for quantification of gene expression. Fragment counts were derived using HTS-seq program using mm10 Ensembl transcripts as model. Various QC analyses were conducted to assess the quality of the data and to identify potential outliers. Differentially expressed genes were identied using bioconductor package edgeR at adjusted p-values (FDR) of less than or equal to 0.1.