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.

本数据集专注于研究中枢神经系统条件反射反应。在从皮层中分离神经元之前24小时，对脊髓进行了损伤。随后，细胞在培养皿中分别培养了1天、2天、3天、5天或7天。未经预处理的培养组由未经预先损伤处理的皮层分离的神经元组成。对照组细胞在培养皿中分别培养了1天、2天、3天、5天或7天。随后，提取并处理RNA进行RNA测序。对从总共29只小鼠样本中收集的RNA-seq数据进行对齐概要和后续差异表达分析。使用STAR分节读对齐器将读取片段对齐到最新的小鼠mm10参考基因组。以对齐到小鼠mm10 refSeq参考注释中已知基因区域的读取片段的总计数作为基因表达量量化的基础。使用mm10 Ensembl转录本作为模型，通过HTS-seq程序推导出片段计数。进行了多种质量控制分析以评估数据质量并识别潜在的异常值。使用bioconductor包edgeR在调整后的p值（FDR）小于或等于0.1的情况下识别差异表达基因。