File S1 - The Cultural Divide: Exponential Growth in Classical 2D and Metabolic Equilibrium in 3D Environments

All the supporting information has been collected into one file for the convenience of the reader. The material is presented as an excel spreadsheet to make it easily accessible. In File S1, the information is presented on different tabs. The supporting information is divided into 6 parts: TOC. Table of contents; P1_data. Basic proteomic data. The basic data set; P2_Histogram. Distribution of protein changes against the degree of change. The ratio of change for each protein (in HepG2/C3A cells growing at dynamic equilibrium in 22 day old 3D spheroid cultures divided by that seen in exponentially growing cells grown using the classical 2Dculture) was grouped and the number of proteins in each group was then plotted against the ratio of change. The dotted line is the reciprocal plot to emphasise the skewedness of the distribution. Fold change is expressed as the log2. n = 4; P3. Extended results description. This section provides a detailed explanation for the statements made in the result section. It has multiple tabs corresponding to the headings used in the ‘results’ section; P4_Dot-plot_Spliceosome. The Spliceososme. Spliceosome proteins have been grouped according to subunit structure plotted against their ratio of change (3D/2D). Fold change is expressed as the log2. Error bars are shown and the average is indicated by the broad grey bar. n = 4; P5_Subunit_Statistics. Statistical comparisons of protein expression in macromolecular subcomplexes. Proteins were grouped into sub-complexes and all possible combinations of the groups were compared using a standard two-tailed T test; P6_tRNA-MSC. Comparison of the changes in the ratio of abundance of tRNA synthetases which are part of the MSC complex with those that are not. tRNA synthetases have been grouped according to whether they form part of the MSC complex or not and plotted against their ratio of change (3D/2D). Fold change is expressed as the log2. Error bars are shown and the average is indicated by the broad grey bar. n = 4. (XLSX)