Dahlquist:Yeast Cold Shock
From OpenWetWare
Comparator Expression Datasets
Environmental Stress Response
Cold or Near-freezing
Sahara et al. 2002
- 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
- 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 indpendent 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
Regulatory Networks
- Jothi et al. 2009
Zinc
- De Nicola et al. 2007; Supplemental Data but not complete dataset
Other
- Check with online compendia, Hughes and Princeton
Ribosome Biogenesis Pathway
- 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 |
- 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 |
