Dahlquist:Yeast Cold Shock

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Comparator Expression Datasets

Environmental Stress Response

• Gasch et al. 2000
• Causton et al. 2001

Cold or Near-freezing

Sahara et al. 2002

1. Sahara T, Goda T, and Ohgiya S. Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. J Biol Chem. 2002 Dec 20;277(51):50015-21. DOI:10.1074/jbc.M209258200 |

• Full dataset here
  • Strain: YPH500 (MATα, ura3-52, lys2-801, ade2-101, trp1-Δ63, his3-Δ200, leu2-Δ1)
  • Media: YPD
  • Experimental Conditions
    • t0 is A600 = 2.0, 30°C, shaking 100 rpm
    • shift to 10°C, shaking 100 rpm, t15, t30, t120 (2 h), t240 (4 h), t480 (8 h)
  • Replicates: 2 independent replicates averaged
  • Reference sample: t0
  • Methods: 15 μg total RNA directly labeled, no dye-swap control except for t0-t0 self-hybe, cDNA microrray

Schade et al. 2004

2. Schade B, Jansen G, Whiteway M, Entian KD, and Thomas DY. Cold adaptation in budding yeast. Mol Biol Cell. 2004 Dec;15(12):5492-502. DOI:10.1091/mbc.e04-03-0167 |

• Partial dataset here; have complete dataset from author
  • Strains: BY4743 (Mata/Matα, wild type), BSY25 (BY4743, homozygous Δmsn2::kanMX ΔMSN4::kanMX met15)
  • Media: YPD
  • Experimental conditions
    • t0 is A600 = 0.6, 30°C, shaking 170 rpm, shift to 10°C, shaking 170 rpm, t10, t30, t120 (2 h)
    • t0 is A600 = 0.4, 30°C, shaking 170 rpm, shift to 10°C, shaking 170 rpm, t720 (12 h)
    • t0 is A600 = 0.1, 30°C, shaking 170 rpm, shift to 10°C, shaking 170 rpm, t3600 (60 h)
  • Replicates: t0 (2 rep), t10 (3 rep), t30 (3 rep), t120 (2 rep), t720 (2 rep), t3600 (3 rep)
  • Reference sample: not stated in paper, assumed to be t0, so the t0 arrays were self-self hybe?
  • Methods: 3 μg mRNA directly labeled, dye swap performed, "genomic" microarray, obtained from University Health Network (so likely cDNA)

Kandror et al. 2004

• Kandror et al. 2004; dataset not available
  • Strains: "wild type", specific strain not stated
  • Media: YPGal
  • Experimental conditions
    • "mRNA samples from yeast growing at 30°C or 0°C for 24 hours were analyzed by whole-genome microarray hybridization"
    • Replicates: 2 independent replicates averaged
    • That's all the information provided in paper.

Murata et al. 2006

• Murata et al. 2006; Some data available here
  • Strain: S288c (MATα SUC2 mal mel gal2 CUP1)
  • Media: YPD
  • Experimental conditions
    • t0 is A660 = 0.5, 25°C, shaking 120-130 rpm, shift to 4°C, shaking 120-130 rpm, t360 (6 h), t720 (12 h), t1440 (24 h), t2880 (48 h)
    • Replicates: 5 independent cultures
    • Reference sample: A660 = 1.0 (25°C?)
  • Methods: 1-2 μg mRNA directly labeled, cDNA microarray, no dye swap
• Tai et al. 2007
  • Strain: CEN.PK113-7D (MATa)
  • Media: defined synthetic medium limited by carbon or nitrogen with all other growth requirements in excess
  • Experimental conditions
    • dilution rate of 0.03 h^-1, stirrer 600 rpm
    • Carbon-limiting at 12°C or 30°C; nitrogen limited at 12°C or 30°C; all were anaerobic; steady-state growth
    • Replicates: 3 independent replicates for each condition
    • Reference sample: none because Affymetrix chips
  • Methods: Affymetrix methods

Beltran et al. 2006

• Beltran et al. (2006); dataset here

Pizarro et al. 2008

• Pizarro et al. 2008; Supplemental Data

Regulatory Networks

• Jothi et al. 2009
  • Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture;
  • Supplemental Data
• Zhu et al. 2009

1. Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy T, Labaer J, and Bulyk ML. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res. 2009 Apr;19(4):556-66. DOI:10.1101/gr.090233.108 |

Other

• Check with online compendia, Hughes and Princeton

Zinc

1. De Nicola R, Hazelwood LA, De Hulster EA, Walsh MC, Knijnenburg TA, Reinders MJ, Walker GM, Pronk JT, Daran JM, and Daran-Lapujade P. Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures. Appl Environ Microbiol. 2007 Dec;73(23):7680-92. DOI:10.1128/AEM.01445-07 |
2. Rutherford JC and Bird AJ. Metal-responsive transcription factors that regulate iron, zinc, and copper homeostasis in eukaryotic cells. Eukaryot Cell. 2004 Feb;3(1):1-13. DOI:10.1128/EC.3.1.1-13.2004 |
3. Rutherford JC, Chua G, Hughes T, Cardenas ME, and Heitman J. A Mep2-dependent transcriptional profile links permease function to gene expression during pseudohyphal growth in Saccharomyces cerevisiae. Mol Biol Cell. 2008 Jul;19(7):3028-39. DOI:10.1091/mbc.e08-01-0033 |
4. Wu CY, Bird AJ, Chung LM, Newton MA, Winge DR, and Eide DJ. Differential control of Zap1-regulated genes in response to zinc deficiency in Saccharomyces cerevisiae. BMC Genomics. 2008 Aug 1;9:370. DOI:10.1186/1471-2164-9-370 |
5. Eide DJ. Homeostatic and adaptive responses to zinc deficiency in Saccharomyces cerevisiae. J Biol Chem. 2009 Jul 10;284(28):18565-9. DOI:10.1074/jbc.R900014200 |
6. Eide DJ. Zinc transporters and the cellular trafficking of zinc. Biochim Biophys Acta. 2006 Jul;1763(7):711-22. DOI:10.1016/j.bbamcr.2006.03.005 |
7. Eide DJ, Clark S, Nair TM, Gehl M, Gribskov M, Guerinot ML, and Harper JF. Characterization of the yeast ionome: a genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae. Genome Biol. 2005;6(9):R77. DOI:10.1186/gb-2005-6-9-r77 |
8. Eide DJ. Multiple regulatory mechanisms maintain zinc homeostasis in Saccharomyces cerevisiae. J Nutr. 2003 May;133(5 Suppl 1):1532S-5S. DOI:10.1093/jn/133.5.1532S |

• De Nicola et al. 2007; Supplemental Data but not complete dataset
• Zip file containing Sc_ZincIonHomeostasis.mapp

Ribosome Biogenesis Pathway

1. Fatica A and Tollervey D. Making ribosomes. Curr Opin Cell Biol. 2002 Jun;14(3):313-8. DOI:10.1016/s0955-0674(02)00336-8 |
2. Li Z, Lee I, Moradi E, Hung NJ, Johnson AW, and Marcotte EM. Rational extension of the ribosome biogenesis pathway using network-guided genetics. PLoS Biol. 2009 Oct;7(10):e1000213. DOI:10.1371/journal.pbio.1000213 |
3. Wade CH, Umbarger MA, and McAlear MA. The budding yeast rRNA and ribosome biosynthesis (RRB) regulon contains over 200 genes. Yeast. 2006 Mar;23(4):293-306. DOI:10.1002/yea.1353 |

• Zip file containing Sc_RibosomeBiogenesis.mapp