Open Access Research

Characterization of the yeast ionome: a genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae

David J Eide1*, Suzanne Clark1, T Murlidharan Nair2, Mathias Gehl3, Michael Gribskov2, Mary Lou Guerinot4 and Jeffrey F Harper3

Author Affiliations

1 Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA

2 San Diego Supercomputer Center, University of California-San Diego, La Jolla, CA 92903, USA

3 Biochemistry Department, University of Nevada, Reno, Nevada 89557, USA

4 Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA

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Genome Biology 2005, 6:R77  doi:10.1186/gb-2005-6-9-r77

Published: 30 August 2005

Additional files

Additional data file 1:

The mutant strains assayed in the first-pass (n = 1), second-pass (n = 3), and third-pass (n = 6) inductively coupled plasma-atomic emission spectroscopy (ICP-AES) analyses are listed. Genes identified by genome sequencing or other studies that were not analyzed are also listed.

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Additional data file 2:

Shown are the results of the third-pass (n = 6) inductively coupled plasma-atomic emission spectroscopy (ICP-AES) analysis. Sheet 1: Normalized concentrations in parts per million (ppm) for each of the 13 elements assayed. Sheet 2: z scores are reported for each mutant and each element. These values are the number of standard deviations that the mutant value differed from the mean of the wild-type samples included in that experiment. Sheet 3: The z score data from Sheet 2 were converted into trinary data. A value of 1 was assigned if the z score was ≥2.5 and -1 if the z score was ≤-2.5. Values of 0 were assigned for values that fell between those boundaries.

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Additional data file 3:

The descriptions of gene function were obtained from the Saccharomyces Genome Database [43].

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Additional data file 4:

Shown are the results of an inductively coupled plasma-atomic emission spectroscopy (ICP-AES) analysis (n = 6) of V-ATPase subunit mutants grown in yeast extract-peptone-dextrose (YPD) medium with metal supplements. Normalized accumulation is reported in parts per million (ppm) and z scores are reported for each element. Calcium values from this experiment are not reported due to a high background of this element in these particular samples.

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Additional data file 5:

Shown are the results of an inductively coupled plasma-atomic emission spectroscopy (ICP-AES) analysis (n = 6) of wild-type cells grown in yeast extract-peptone-dextrose (YPD) medium with or without the metal supplements. Normalized accumulation is reported in parts per million (ppm) and z scores are reported for each element.

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