Growth-limiting intracellular metabolites in yeast under diverse nutrient limitations
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  • Dataset 1 - Metabolite data as tab-delimited text. KEGG IDs are also provided. Values are log2-ratios to those obtained in the reference chemostats for this study (phosphate at 0.05 h-1).
  • Dataset 2 - Transcript data as tab-delimited text. KNN-imputed. (This file contains only the conditions that match the metabolite data: for the full data set, with clustering information, see the Brauer et al supplement.) Values are log2-ratios to those obtained in the reference (growth on glucose at 0.25 h-1).
  • Dataset 3 - Ion counts for each individual sample, including both filter and pellet preparations, normalized by total cell volume and the volume of the extraction solvent. These data were collapsed to give Dataset 1, by taking the median log2-ratio of the experimental sample counts to the reference counts (see Materials and Methods).

  • Supplementary Table S1 - Metabolites analyzed and their associated mass spectrometry parameters. In the Excel workbook, the tab "Compounds_included" provides ionization mode, parent ion mass, product ion mass, collision energy, and chromatography retention time for all compounds that were successfully measured. Compounds that were measured unsuccessfully (e.g., did not yield acceptable signal-to-noise from biological samples) are listed separately under the tab "Compounds_excluded."
  • Supplementary Table S2 - Comparison of metabolite yields as a function of the cell harvesting method and composition of the extraction solvent. A two-by-two comparison of cell harvesting method ("MeOH quench" versus "filters") and extraction solvent composition ("MeOH" versus "ACN") was performed, using yeast growing exponentially in glucose minimal media (N = 3 independent cultures for each condition). In the Excel workbook, raw data (ion counts) are provided in the first tab, and specific head-to-head comparisons in the subsequent tabs (e.g., the second tab, entitled "Filters-Extract MeOH vs ACN" is a head-to-head comparison, for cells collected by the filtration approach, of the two extraction solvent compositions). The term "MeOH quench" refers to quenching cells in methanol and then isolating the quenched cells by centrifugation; the term "filters" refers to isolating the cells directly by vacuum filtration. The solvent composition "MeOH" refers to 80:20 methanol:water; "ACN" refers to 40:40:20 acetonitrile:methanol:water.
  • Supplementary Table S3 - Chemostat properties: dilution rate, klett, cell count, cell volume, and extracellular nutrient concentrations.

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