Supplementary files supporting the paper 'Microarray profiling emphasizes transcriptomic differences between hippocampal in vivo tissue and in vitro cultures'

Differential expression was performed using the R package 'limma' (R package version 3.44.3) (Supplementary files 1-4; 1_diff_expr_WT_cell_vs_tissue, 2_diff_expr_101LL_cell_vs_tissue, 3_diff_expr_cell_WT_ vs_101LL, 4_diff_expr_tissue_WT_ vs_101LL) and gene ontology analysis was performed using the R package 'topGO' (R package version 2.40.0) (Supplementary files 5-6; 5_go_all_bp_WT_cell_vs_tissue, 6_go_all_bp_101LL_cell_vs_tissue). Primary hippocampal cell cultures are routinely used as an experimentally accessible model platform for the hippocampus and brain tissue in general. Containing multiple cell types including neurons, astrocytes and microglia in a state that can be readily analysed optically, biochemically and electrophysiologically, such cultures have been used in many in vitro studies. To what extent the in vivo environment is recapitulated in primary cultures in an on-going question. Here we compare the transcriptomic profiles of primary hippocampal cell cultures and intact hippocampal tissue. In addition, by comparing profiles from wild type and the PrP 101LL transgenic model of prion disease, we also demonstrate that gene conservation is predominantly conserved across genetically altered lines.

本研究采用R包‘limma’（版本3.44.3）完成差异表达分析（补充文件1-4：1_diff_expr_WT_cell_vs_tissue、2_diff_expr_101LL_cell_vs_tissue、3_diff_expr_cell_WT_vs_101LL、4_diff_expr_tissue_WT_vs_101LL），并借助R包‘topGO’（版本2.40.0）开展基因本体（Gene Ontology）分析（补充文件5-6：5_go_all_bp_WT_cell_vs_tissue、6_go_all_bp_101LL_cell_vs_tissue）。原代海马细胞培养物通常作为海马乃至全脑组织的实验可及模型平台被广泛应用。该培养体系包含神经元、星形胶质细胞与小胶质细胞等多种细胞类型，其细胞状态可通过光学、生化及电生理手段便捷表征，已被大量体外研究采用。原代培养体系在多大程度上能够重现体内真实环境，是学界持续探讨的科学问题。本研究对原代海马细胞培养物与完整海马组织的转录组谱展开对比分析。此外，通过对比野生型（Wild Type, WT）与朊病毒疾病PrP 101LL转基因模型的转录组谱，本研究证实基因保守性在遗传修饰的模型系中普遍存在。