Affymetrix GeneChip Yeast Genome S98 [YG_S98]

Genome Wide analysis of mRNAs regulated by the nonsense-mediated  5' to 3' mRNA decay pathways in yeast.

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To determine the effects of inactivation of both the nosense-mediated mRNA decay pathway and the general 5' to 3' decay pathway on yeast mRNA decay, we compared the expression profiles of the wild-type, xrn1, xrn1 upf1, xrn1 nmd2, and xrn1 upf3 strains.

genotype

Transcription profiling by array of yeast mutants

Transcription profiling of yeast wild type, xrn1, xrn1 upf1, xrn1 nmd2, and xrn1 upf3 strains to investigate mRNA decay

To determine the effects of inactivation of both the nosense-mediated mRNA decay pathway and the general 5' to 3' decay pathway on yeast mRNA decay, we compared the expression profiles of the wild-type, xrn1, xrn1 upf1, xrn1 nmd2, and xrn1 upf3 strains.


Affymetrix:Protocol:Hybridization-EukGE-WS2v4[]

Title: Affymetrix EukGE-WS2v4 Hybridization. Description:

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-AFFY-7

P-MEXP-1343

Yeast cells were grown in liquid YEPD medium at 30ºC to an OD600 of 0.7.

P-MEXP-1344

Cultures (10 ml) were harvested by centrifugation, cell pellets were frozen on dry ice, and the pellets were then stored at -80ºC until RNA was isolated.

P-MEXP-1345

Total RNA was isolated from frozen cell pellets by the hot phenol method described previously (He and Jacobson,1995,Genes Dev 9:437-454). Total RNA (100ug) from each sample was spiked with five poly(A)-tagged control RNAs trp, thr, dap, phe, and lys at a concentration of 4, 13.3, 40, 133.3, and 400 pmol/mg respectively. The spiked total RNA was further purified from an affinity resin (RNeasy, QIAGEN). mRNA, when used, was purified from total RNA with an oligo(dT) selection step(Oligotex, QIAGEN). RNA integrity was assessed by either northern blotting or by gel electrophoresis.  

Transcription profiling by array of yeast mutants

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