Additional file 1 of Evaluating oleaginous yeasts for enhanced microbial lipid production using sweetwater as a sustainable feedstock
Creators: name: Keita, Valériane Malika
name: Lee, Yi Qing
name: Lakshmanan, Meiyappan
name: Ow, Dave Siak-Wei
name: Staniland, Paul
name: Staniland, Jessica
name: Savill, Ian
name: Tee, Kang Lan
name: Wong, Tuck Seng
name: Lee, Dong-Yup
Publisher: name: figshare
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Ecology

description: Additional file 1: Figure S1. Aspect and properties of the three types of sweetwater used in this study. The asterisk indicates that SW85 was diluted before pH measurement. Figure S2. Bar graphs of data shown in Table 2. Error bars indicate standard deviations. Figure S3. Evaluating the glycerol tolerance of oleaginous yeasts Cells were grown in 96-well microplates containing either refined glycerol diluted with synthetic complete nutrient mix for a final glycerol concentration of 2% (w/v) [black line: Gly2SC], 8% (w/v) [blue line: Gly8SC] or 16% (w/v) [red line: Gly16SC]. Cells were grown in quadruplicates and the averages OD600 and associated standard deviations were plotted against time. Figure S4. Bar graphs of data comparing growth in SW35&gt;1.5SC and SW35SC shown in Table 3. Error bars indicate standard deviations. Figure S5. Bar graphs of data comparing pH 6.09 and pH 3.95 in SW15 shown in Table 3. Error bars indicate standard deviations. Figure S6. Evaluating growth in different type of sweetwater diluted with the synthetic complete nutrient mic. Cells were grown in 96-well microplates containing either in SW15 [black line: SW15&gt;1.5SC], SW35 [teal line: SW35&gt;1.5SC] or SW85 [purple line: SW85&gt;1.5SC] diluted in synthetic complete nutrient mix for a final glycerol concentration of 1.5% (w/v). Cells were grown in quadruplicates and the averages OD600 and associated standard deviations were plotted against time. Figure S7. Evaluating effect of sweetwater pH on growth. Cells were grown in 96-well microplates containing either sweetwater with a 15% (w/v) glycerol content at native pH [black line: SW15 pH 3.95] or sweetwater with a 15% (w/v) glycerol content with a pH adjusted to 6 [teal line: SW15 pH 6.09]. Cells were grown in quadruplicates and the averages OD600 and associated standard deviations were plotted against time. Figure S8. Clustergram of sample-to-sample Euclidean distances based on expression counts normalized by variance stabilizing transformation. Figure S9. Growth curves of R. toruloides NRRL Y-6987 in the 4 media used for the transcriptomic analysis. Table S1. Annotation of genes represented in the Fig. 3. Table S2. Top 50 of annotated genes contributing the most to PC1 in the differential expression analysis of SW15 vs Gly15. Gene ranks in terms of contribution to PC1 were given in column Rank #, and genes were sorted by descending contribution in each category. The smallest rank corresponds to the highest the contribution. LFC (Log2 fold change) gives the estimated change between gene expression level of in SW15 compared to Gly15 (Ctrl). This change is associated with a FDR adjusted p-value either non-significant (ns), non-computed (na), lower than 0.01 (&lt; 0.01), between 0.01 and 0.05 (&lt; 0.05) or between 0.05 and 0.1 (&lt; 0.1). Only padj &lt; 0.01 were considered significant in the manuscript. Table S3. Differential expression results of SW15 vs. Gly15 of relevant genes associated with lipid metabolism. Gene ranks in terms of contribution to PC1 were given in column Rank # and genes were sorted by descending contribution in each category. LFC (Log2 fold change) gives the estimated change between gene expression level of in SW15 compared to Gly15 (Ctrl). This change is associated with a FDR adjusted p-value either non-significant (ns), non-computed (na), lower than 0.01 (&lt; 0.01), between 0.01 and 0.05 (&lt; 0.05) or between 0.05 and 0.1 (&lt; 0.1). Only padj &lt; 0.01 were considered significant in the manuscript.