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. 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 |

Zinc

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

Other

• Check with online compendia, Hughes and Princeton

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