GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE19120 Query DataSets for GSE19120
Status Public on Apr 09, 2010
Title Bulk Segregant Analysis Reveals a Novel Xylose Utilization Gene from Saccharomyces cerevisiae
Organism Saccharomyces cerevisiae
Experiment type Genome variation profiling by genome tiling array
Summary To determine the genomic location of a gene that permits xylose utilization we conducted bulk segregant analysis (BSA) using Affymetrix yeast tiling arrays. BSA works by taking advantage of DNA sequence polymorphisms between different strains and the fact that it is relatively easy to pool large numbers of meiotic spore products (segregants) in yeast. Pooling segregants based on their phenotype allows the region of the genome responsible for the phenotype to be detected. This is because DNA polymorphisms in regions unlinked to the locus causing the phenotype will segregate randomly and be “evened” out, while around the genomic region of interest, sequences or polymorphisms responsible for the trait will be present in all positive segregants, and absent in all negative segregants. In our case, a Simi White wine strain (S. cerevisiae) carrying the locus responsible for xylose utilization was crossed to a laboratory strain of Saccharomyces cerevisiae; this strain was estimated to carry DNA polymorphisms relative to the laboratory strain at a level of approximately .5%. Spores from the Simi White / S288c diploid were screened for the xylose utilization phenotype and 39 positive spores were combined into one pool and 39 negative spores into another pool, and genomic DNA (gDNA) was isolated from each pool. We then hybridized the positive and negative gDNA pools to tiling microarrays that were based on the S288c reference genome with the expectation that regions of the genome derived from Simi White will hybridize less robustly to the array because of the DNA polymorphisms between Simi White and S288c. Log2 ratios of probe intensities were calculated (negative/positive), and a peak appeared in the chromosome XV right subtelomeric region that corresponds to less robust hybridization to the microarray of the positive pool gDNA coming from this region of the genome
Overall design gDNA isolated from 39 pooled "xylose positive" S. cerevisiae segregants from ("Simi White" x S288c) compared to gDNA isolated from 39 pooled "xylose negative" segregants from the same cross
Contributor(s) Wenger JW, Schwartz K, Sherlock G
Citation(s) 20485559
Submission date Nov 20, 2009
Last update date Jan 09, 2016
Contact name Gavin Sherlock
Phone 650 498 6012
Fax 650 724 3701
Organization name Stanford University
Department Genetics
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
Platforms (1)
GPL7250 [Sc03b_MR] Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array
Samples (1)
GSM474243 Simi White (788) Positive Pool vs Negative Pool
This SubSeries is part of SuperSeries:
GSE19121 Xylose Utilization Gene in Saccharomyces cerevisiae
BioProject PRJNA123761

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
GSE19120_RAW.tar 100.8 Mb (http)(custom) TAR (of CEL, TXT)
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap