Comparison of sampling techniques for parallel analysis of transcript and metabolite levels in Saccharomyces cerevisiae

Yeast

Volumn 24, Issue 3, 2007, Pages 181-188

  Martins, Ana Margarida ^a   Sha, Wei ^a   Evans, Clive ^a   Martino Catt, Susan ^a   Mendes, Pedro ^a   Shulaev, Vladimir ^a  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

Author keywords

Fast sampling; Fermentors; Metabolome; Microarrays; RNA; Saccharomyces cerevisiae; Transcriptomics

Indexed keywords

METHANOL; PROTEOME; RNA; TRANSCRIPTOME;

ARTICLE; CAPILLARY ELECTROPHORESIS; CELL SEPARATION; CELL STRUCTURE; FREEZE DRYING; FUNGUS CULTURE; MATHEMATICAL MODEL; METABOLITE; METABOLOMICS; MICROARRAY ANALYSIS; NONHUMAN; PARALLEL DESIGN; PRIORITY JOURNAL; PROTEIN ANALYSIS; SACCHAROMYCES CEREVISIAE; SAMPLING; SUCROSE DENSITY GRADIENT CENTRIFUGATION; TRANSCRIPTOMICS; ULTRAVIOLET SPECTROSCOPY;

CENTRIFUGATION; CRYOPROTECTIVE AGENTS; FREEZING; GLYCINE; METHANOL; RNA, FUNGAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES CEREVISIAE;

EID: 34047242069     PISSN: 0749503X     EISSN: 10970061     Source Type: Journal    
DOI: 10.1002/yea.1442     Document Type: Article

References (23)

1. Affymetrix. 2004. Eukaryotic target preparation. In GeneChip Expression Analysis Technical Manual. Affymetrix: Santa Clara, CA.
2. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57: 289-300.
3. Castrillo JI, Hayes A, Mohammed S, Gaskell SJ, Oliver SG. 2003. An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry. Phytochemistry 62: 929-937.
4. Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323-337.
5. Chance B, Eisenhardt RH, Gibson QH, Louberg-Holm KK (eds). 1964. Rapid Mixing and Sampling Techniques in Biochemistry. Academic Press: New York.
6. Chen D, Toone WM, Mata J, et al. 2003. Global transcriptional responses of fission yeast to environmental stress. Mol Biol Cell 14: 214-229.
7. de Koning W, van Dam K. 1992. A method for the determination of changes of glycolytic metabolites in yeast on a subsecond time scale using extraction at neutral pH. Anal Biochem 204: 118-123.
8. Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241-4257.
9. Gonzalez B, Francois J, Renaud M. 1997. A rapid and reliable method for metabolite extraction in yeast using boiling buffered ethanol. Yeast 13: 1347-1355.
10. Griffin TJ, Gygi SP, Ideker T, et al. 2002. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteom 1: 323-333.
11. Gygi SP, Rochon Y, Franza BR, Aebersold R. 1999. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19: 1720-1730.
12. Hatzimanikatis V, Lee KH. 1999. Dynamical analysis of gene networks requires both mRNA and protein expression information. Metab Eng 1: 275-281.
13. Ideker T, Thorsson V, Ranish JA, et al. 2001. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292: 929-934.
14. Manna F, Massardo DR, Del Giudice L, Alifano P, Wolf K. 1996. A simple and inexpensive method for RNA extraction from yeasts. Trends Genet 12: 337-338.
15. Qiagen. 2003. RNeasy MinElute Cleanup Handbook. Quiagen: Valencías, CA.
16. Rivas R, Vizcaino N, Buey RM, et al. 2001. An effective, rapid and simple method for total RNA extraction from bacteria and yeast. J Microbiol Methods 47: 59-63.
17. Schaefer U, Boos W, Takors R, Weuster-Botz D. 1999. Automated sampling device for monitoring intracellular metabolite dynamics. Anal Biochem 270: 88-96.
18. Schmitt ME, Brown TA, Trumpower BL. 1990. A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res 18: 3091-3092.
19. Schroeder A, Mueller O, Stocker S, et al. 2006. The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol 7: 3.
20. Theobald U, Mailinger W, Reuss M, Rizzi M. 1993. In vivo analysis of glucose-induced fast changes in yeast adenine nucleotide pool applying a rapid sampling technique. Anal Biochem 214: 31-37.
21. Villas-Boas SG, Hojer-Pedersen J, Akesson M, Smedsgaard J, Nielsen J. 2005. Global metabolite analysis of yeast: evaluation of sample preparation methods. Yeast 22: 1155-1169.
22. Warburg O, Christian W. 1942. Isolation and crystallization of enolase. Biochem Z 310: 384-421.
23. Weckwerth W, Wenzel K, Fiehn O. 2004. Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks. Proteomics 4: 78-83.