C99 overexpression in independent cell clones. SH-SY5Y cells were stably transfected with a pCEP-vector containing the amyloid precursor protein C-terminal fragment C99WT, and constructs bearing the point mutations C99I45F and C99V50F. The same cell line was transfected with an empty vector (negative control). Eight clones (clone 1–3 for C99WT, clone 1–3 for C99I45F and clone 1–2 for C99V50F) with approximately similar expression levels and C99V50F clone 3, showing stronger expression, were selected and used for transcriptome and proteome analysis. Apart from analyzing the complete set of three clones, data analysis for the transcriptomic approach was also performed by excluding clone 3 (C99V50F) resulting in no significant difference compared to the triplicates.