Dahlquist:Yeast Cold Shock: Difference between revisions
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*Pub med reference = 15368892 | *Pub med reference = 15368892 | ||
*Strains: CEN.PK113-7D and EC1118 | *Strains: CEN.PK113-7D and EC1118 | ||
*Media: Nitrogen-limited, anaerobic cultures | |||
==== Becerra et al. 2003 ==== | ==== Becerra et al. 2003 ==== |
Revision as of 11:17, 30 October 2012
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
- 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
- Strain: QA23
- Media: YEPD
Pizarro et al. 2008
- Pizarro et al. 2008; Supplemental Data
- Pub med reference = 15368892
- Strains: CEN.PK113-7D and EC1118
- Media: Nitrogen-limited, anaerobic cultures
Becerra et al. 2003
- Becerra Article Link
- Pub med reference = 18629074
Regulatory Networks
- Jothi et al. 2009
- Zhu et al. 2009
- Pub med reference = 19158363
Other
- Check with online compendia, Hughes and Princeton
Zinc
- 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.
- Supplemental Data but not complete dataset
- 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.
- 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.
- 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.
- Eide DJ. (2009) Homeostatic and adaptive responses to zinc deficiency in Saccharomyces cerevisiae. J Biol Chem. 284(28):18565-18569.
- Eide DJ. (2006) Zinc transporters and the cellular trafficking of zinc. Biochim Biophys Acta. 1763(7):711-722.
- 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.
- Eide DJ. (2003) J Nutr. Multiple regulatory mechanisms maintain zinc homeostasis in Saccharomyces cerevisiae. 133(5 Suppl 1):1532S-1535S.
Ribosome Biogenesis Pathway
- Fatica 2002
- Pub med reference = 12067653
- Zhihua 2009
- Pub med reference = 19806183
- Wade 2006
- Pub med reference = 16544271
- 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 [1]
- 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 [2]
- 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 [3]
- 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 [4]
- 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 [5]
- 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[6]