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Series GSE37254 Query DataSets for GSE37254
Status Public on Apr 17, 2012
Title Functional profiling in yeast with zinc-limitation
Organism Saccharomyces cerevisiae
Experiment type Other
Summary Zinc is an essential nutrient because it is a required cofactor for many enzymes and transcription factors. To discover genes and processes in yeast that are required for growth when zinc is limiting, we used genome-wide functional profiling. As a result, we identified over 400 different genes required for optimal growth under zinc-limiting conditions. Among these were several targets of the Zap1 zinc-responsive transcription factor. Their importance is consistent with their up-regulation by Zap1 in low zinc. We also identified genes that implicate Zap1-independent processes as important. These include endoplasmic reticulum function, oxidative stress resistance, vesicular trafficking, peroxisome biogenesis, and chromatin modification. Our studies also indicated the critical role of macroautophagy in low zinc growth. Finally, as a result of our analysis, we discovered a previously unknown role for the ICE2 gene in maintaining ER zinc homeostasis.
 
Overall design Pools of homozygous diploid deletion mutants (n = 4,607 strains) were grown in zinc defined media (LZM) at 2 concentrations for 5 and 15 generations (5g, 15g).
Each strain has a deletion in a different gene. In each strain, the gene was replaced by a deletion cassette containing a antibiotic resistance gene and two BARCODES, up and down tags (Please see Giaever et al, 2002, Nature). These tags in the DNA are specific to each strain. We pool all deletion strains and grow them under a selective condition; extract DNA; amplify barcodes using universal primers and hybridize to arrays containing complemetary sequences to the up and down tags. In this way, we can look at growth of each of the strains. Our strategy is to analyze separately the up and down tags. Therefore, for each array (CEL file), we generate two data files, one for all ups and another one for all downs. In these files, the list of genes are the same but the data come from different set of probes, up or down. The values are log2 averages of replicate probes for the same tag. These pre processed files were used to identify strains with differential growth in 1uM zinc by comparing to the 100uM zinc arrays.
 
Contributor(s) NORTH M, STEFFEN J, LOGUINOV AV, ZIMMERMAN GR, VULPE CD, EIDE DJ
Citation(s) 22685415
Submission date Apr 13, 2012
Last update date Mar 13, 2013
Contact name Chris Vulpe
E-mail(s) vulpe@berkeley.edu
Phone 510-642-1834
Organization name UC Berkeley
Department Nutritional Sciences and Toxicology
Lab Vulpe
Street address 119 Morgan Hall
City Berkeley
State/province Ca
ZIP/Postal code 94720
Country USA
 
Platforms (1)
GPL8858 Affymetrix S. cerevisiae TAG4 101K array [condensed version]
Samples (48)
GSM914191 Homozygous pool-5 generations-1uM zinc-replicate1-Down
GSM914192 Homozygous pool-5 generations-1uM zinc-replicate1-Up
GSM914236 Homozygous pool-5 generations-1uM zinc-replicate2-Down
Relations
BioProject PRJNA159393

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE37254_RAW.tar 33.0 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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