Dahlquist:Yeast Cold Shock

Environmental Stress Response

 * Gasch et al. 2000
 * Causton et al. 2001

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
 * [[media: Shade paper gene map.zip | 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

 * Beltran et al. (2006); dataset here
 * Full Beltran Article

Pizarro et al. 2008

 * Pizarro et al. 2008; Supplemental Data
 * Pub med reference = 15368892

Becerra et al. 2003

 * Becerra Article Link
 * Pub med reference = 18629074

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
 * Pub med reference = 19158363

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) * Supplemental Data but not complete dataset
 * 3) 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.
 * 4) 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.
 * 5) 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.
 * 6) Eide DJ. (2009) Homeostatic and adaptive responses to zinc deficiency in Saccharomyces cerevisiae. J Biol Chem. 284(28):18565-18569.
 * 7) Eide DJ. (2006) Zinc transporters and the cellular trafficking of zinc. Biochim Biophys Acta. 1763(7):711-722.
 * 8) 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.
 * 9) Eide DJ. (2003) J Nutr. Multiple regulatory mechanisms maintain zinc homeostasis in Saccharomyces cerevisiae. 133(5 Suppl 1):1532S-1535S.


 * [[Media:Sc_ZincIonHomeostasis_kb3.zip | Zip file containing Sc_ZincIonHomeostasis.mapp]]

Ribosome Biogenesis Pathway

 * Fatica 2002
 * Pub med reference = 12067653
 * Zhihua 2009
 * Pub med reference = 19806183
 * Wade 2006
 * Pub med reference = 16544271
 * [[Media:Sc_RibosomeBiogenesis3.zip | Zip file containing Sc_RibosomeBiogenesis.mapp]]

Genetic Screens

 * Akira 2006
 * Pub med reference = 16989656
 * Fumiyoshi 2008
 * Pub med reference = 18245339

Nitrogen Utilization

 * Magasanik B and Kaiser CA (2002) Nitrogen regulation in Saccharomyces cerevisiae. Gene 290(1-2):1-18
 * This paper outlines the function of GLN3 in the cell in response to poor nitrogen sources
 * Bertram PG, et al. (2002) Convergence of TOR-nitrogen and Snf1-glucose signaling pathways onto Gln3. Mol Cell Biol 22(4):1246-52
 * Outlines the role of glucose and snf1
 * Cox KH, et al. (2004) Actin cytoskeleton is required for nuclear accumulation of Gln3 in response to nitrogen limitation but not rapamycin treatment in Saccharomyces cerevisiae. J Biol Chem 279(18):19294-301
 * Outlines the nonspecific dissociation of Gln3p in the cytoplasm caused by the presence of the actin cytoskeleton
 * Cox KH, et al. (2002) Cytoplasmic compartmentation of Gln3 during nitrogen catabolite repression and the mechanism of its nuclear localization during carbon starvation in Saccharomyces cerevisiae. J Biol Chem 277(40):37559-66
 * Outlines the mechanism of localization for Gln3p during cellular starvation
 * Kulkarni AA, et al. (2001) Gln3p nuclear localization and interaction with Ure2p in Saccharomyces cerevisiae. J Biol Chem 276(34):32136-44
 * Describes Ure2p role in the regulation of the function of Gln3p
 * Patrice Godard (2007) Effect of 21 Different Nitrogen Sources on Global Gene Expression in the Yeast Saccharomyces cerevisiae
 * Outlines the effect of varying nitrogen sources to that of transcriptional response variation