King, Declan. (2021). Supplementary files supporting the paper "Microarray profiling emphasizes transcriptomic differences between hippocampal in vivo tissue and in vitro cultures", [dataset]. University of Edinburgh. Roslin Institute. https://doi.org/10.7488/ds/3015.
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.
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