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Series GSE98349 Query DataSets for GSE98349
Status Public on Apr 29, 2017
Title Mapping of mitotic gene conversion tracts associated with repair of a defined double-strand break (DSB) using SNP microarray
Organism Saccharomyces cerevisiae
Experiment type Genome variation profiling by SNP array
Summary Mitotic recombination between homologous chromosomes can lead to loss-of-heterozygosity (LOH), which is an important contributor to human disease. In the current study, a defined double-strand break (DSB) on chromosome IV was used to initiate LOH in a yeast strain with sequence-diverged chromosomes. Associated gene conversion tracts, which reflect the repair of mismatches formed when diverged chromosomes exchange single strands, were mapped using microarrays. LOH events reflected two broken chromosomes, one of which was repaired as a crossover and the other as a noncrossover.
 
Overall design To examine DSB-induced mitotic gene conversion tracts, an I-SceI cut site was inserted into one of the chromosome IVs of a diploid strain (by mating W303 and YJM789 haploid parents) and cleavage by I-SceI enzyme was induced with 45 or 90 minutes of incubation with 2% galactose. Twenty independent DSB-induced red white sectored colonies were analyzed using SNP microarrays specific for yeast chromosome IV. To determine the heterozygous versus homozygous status of SNPs in each event, DNA from individual red or white sectors was labeled with Cy5 and mixed with control parental DNA labeled with Cy3. Following competitive hybridization of the mixed samples to the microarray, the ratio of Cy5 to Cy3 hybridization to each oligo was determined. A hybridization ratio of ~1 to both W303- and YJM879-specific oligos signals heterozygosity for the corresponding SNP. A hybridization ratio >1.5 for a haploid-specific oligo indicates homozygosity for the corresponding SNP, while a ratio <0.5 for the alternative haploid specific indicates loss of the corresponding SNP.
 
Contributor(s) Hum YF, Jinks-Robertson S
Citation(s) 28743762
Submission date Apr 28, 2017
Last update date Jul 25, 2021
Contact name Yee Fang Hum
E-mail(s) yfhum728@gmail.com
Phone 9196845891
Organization name Duke University
Department Molecular Genetics and Microbiology
Lab Jinks-Robertson
Street address 381 CARL Building
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platforms (1)
GPL21553 Agilent-031671 Chr4 RA V2 027289 (SPOT_ID version)
Samples (40)
GSM2592538 SJR4317-sectored_1R
GSM2592539 SJR4317-sectored_1W
GSM2592540 SJR4317-sectored_2R
Relations
BioProject PRJNA384791

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
GSE98349_RAW.tar 59.5 Mb (http)(custom) TAR (of GPR)
Processed data included within Sample table

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