Expression data from WT and Neu1 deficient 1 mo and 5 mo hippocampi. Expression data from WT and Neu1 deficient 1 mo and 5 mo hippocampi

Microarray data was used to assess progressive upregulation of genes during course of disease in Neu1 deficient mice and use for GSEA studies to assess upregulated pathways. Top upregulated genes often belonged to the myeloid lineage. Data was used to guide assessment of the neuroinflammatory response that occurs in Neu1 deficient hippocampi. Overall design: Total RNA (100 ng) was extracted from WT and Neu1 deficient hippocampi at 1 and 5 months, converted into biotin-labeled cRNA, and hybridized to a mouse Affymetrix GeneChip. Probe signals from microarrays were normalized and transformed into log2 transcript expression values by using the Robust Multiarray Average algorithm. Differentially expressed transcripts were identified by ANOVA, and the false discovery rate (FDR) was estimated. GSEA were completed using xtools software.

本研究利用微阵列（microarray）数据，分析Neu1缺陷小鼠病程中基因的渐进性上调特征，并将该数据应用于基因集富集分析（Gene Set Enrichment Analysis, GSEA）以筛选上调通路。上调幅度最为显著的基因多隶属于髓系细胞谱系。本数据集还用于辅助评估Neu1缺陷小鼠海马体中出现的神经炎症反应。
实验设计：分别于1月龄和5月龄时，从野生型（Wild Type, WT）及Neu1缺陷小鼠的海马体中提取总RNA（100 ng），将其反转录为生物素标记的互补RNA（cRNA）后，与小鼠Affymetrix基因芯片进行杂交。采用稳健多阵列平均（Robust Multiarray Average, RMA）算法对微阵列的探针信号进行标准化处理，并转换为以log2为底的转录本表达值。通过方差分析（Analysis of Variance, ANOVA）筛选差异表达转录本，并估算错误发现率（False Discovery Rate, FDR）。使用xtools软件完成基因集富集分析（GSEA）。