Dahlquist:Yeast Cold Shock

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== Ribosome Biogenesis Pathway ==
== Ribosome Biogenesis Pathway ==
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*[http://www.sciencedirect.com/science/article/pii/S0955067402003368 Fatica 2002]
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<biblio>
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**Pub med reference = 12067653
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#Paper1 pmid=12067653
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*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2749941/?tool=pubmed Zhihua 2009]
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#Paper2 pmid=19806183
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**Pub med reference = 19806183
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#Paper3 pmid=16544271
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*[http://onlinelibrary.wiley.com/doi/10.1002/yea.1353/full Wade 2006]
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</biblio>
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**Pub med reference = 16544271
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* [[Media:Sc_RibosomeBiogenesis3.zip | Zip file containing Sc_RibosomeBiogenesis.mapp]]
* [[Media:Sc_RibosomeBiogenesis3.zip | Zip file containing Sc_RibosomeBiogenesis.mapp]]

Revision as of 19:14, 25 May 2011

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Contents

Comparator Expression Datasets

Environmental Stress Response

Cold or Near-freezing

Sahara et al. 2002

  • Pub med reference = 12379644
  • Full Sahara Paper Here
  • 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

  • Pub med reference = 15483057
  • Full Schade Article Here
  • Cold Shock Map GenMAPP
  • 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

  • Full Kandror Article; 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

  • Full Murata Article Found Here
  • 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
  • Pub med reference = 17928405
  • 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

Pizarro et al. 2008

Becerra et al. 2003

Regulatory Networks

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, Daran-Lapujade P. (2007) Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures.Appl Environ Microbiol. 73(23):7680-7692.
  2. Rutherford JC, Bird AJ. (2004) Metal-responsive transcription factors that regulate iron, zinc, and copper homeostasis in eukaryotic cells. Eukaryot Cell. 3(1):1-13.
  3. Rutherford JC, Chua G, Hughes T, Cardenas ME, Heitman J. (2008) A Mep2-dependent transcriptional profile links permease function to gene expression during pseudohyphal growth in Saccharomyces cerevisiae. Mol Biol Cell. 19(7):3028-3039.
  4. Wu CY, Bird AJ, Chung LM, Newton MA, Winge DR, Eide DJ. (2008) Differential control of Zap1-regulated genes in response to zinc deficiency in Saccharomyces cerevisiae. BMC Genomics. 9:370.
  5. Eide DJ. (2009) Homeostatic and adaptive responses to zinc deficiency in Saccharomyces cerevisiae. J Biol Chem. 284(28):18565-18569.
  6. Eide DJ. (2006) Zinc transporters and the cellular trafficking of zinc. Biochim Biophys Acta. 1763(7):711-722.
  7. Eide DJ, Clark S, Nair TM, Gehl M, Gribskov M, Guerinot ML, Harper JF. (2005) Characterization of the yeast ionome: a genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae. Genome Biol. 6(9):R77.
  8. Eide DJ. (2003) J Nutr. Multiple regulatory mechanisms maintain zinc homeostasis in Saccharomyces cerevisiae. 133(5 Suppl 1):1532S-1535S.

Ribosome Biogenesis Pathway

Genetic Screens

  1. Ando A, Nakamura T, Murata Y, Takagi H, and Shima J. . pmid:16989656. PubMed HubMed [Paper1]
  2. Abe F and Minegishi H. . pmid:18245339. PubMed HubMed [Paper2]
All Medline abstracts: PubMed HubMed
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