NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2592555 Query DataSets for GSM2592555
Status Public on Apr 29, 2017
Title SJR4317-sectored_9W
Sample type genomic
 
Channel 1
Source name 90-minute DSB induction
Organism Saccharomyces cerevisiae
Characteristics ploidy: diploid (W303 x YJM789)
dsb on chromosome iv: Yes
Treatment protocol 45- or 90-minute of galactose treatment to induce I-SceI cleavage on chromosome IV.
Growth protocol Prior to I-SceI induction, yeast cells were grown overnight at 30°C in 5 ml of non-selective medium containing 1% yeast extract, 2% bacto-peptone and 2% raffinose (YEPR). Following overnight growth, cells were then diluted to an OD of 0.4 in fresh YEPR medium and split into two parallel cultures. When cells reached an OD of 0.8-1, galactose (2% final concentration) was added to one culture of each pair and cells were incubated for an additional 45 or 90 minutes. Following induction for the specified time, yeast cells were pelleted and resuspended in water. Approximately 500 cells/plate were spread on synthetic dextrose medium supplemented with uracil and all amino acids except arginine. Adenine was additionally present at 10 μg/ml, a limiting amount that allows red color development of Ade- cells. Plates were incubated at 30°C overnight and at room temperature for additional 2 days before being moved to 4°C to allow red pigment development.
Extracted molecule genomic DNA
Extraction protocol Cells in each half of a sectored colony were purified by streaking on YEP-glucose medium, and a single colony from each was used for DNA isolation. Genomic DNA was extracted in agarose plugs and then sheared to 200-400 bp by sonication.
Label Cy5
Label protocol DNA from each sector was labeled with Cy5-dUTP and mixed with control parental DNA labeled with Cy3-dUTP.
 
Channel 2
Source name uninduced parental control SJR4317
Organism Saccharomyces cerevisiae
Characteristics ploidy: diploid (W303 x YJM789)
dsb on chromosome iv: No
Treatment protocol 45- or 90-minute of galactose treatment to induce I-SceI cleavage on chromosome IV.
Growth protocol Prior to I-SceI induction, yeast cells were grown overnight at 30°C in 5 ml of non-selective medium containing 1% yeast extract, 2% bacto-peptone and 2% raffinose (YEPR). Following overnight growth, cells were then diluted to an OD of 0.4 in fresh YEPR medium and split into two parallel cultures. When cells reached an OD of 0.8-1, galactose (2% final concentration) was added to one culture of each pair and cells were incubated for an additional 45 or 90 minutes. Following induction for the specified time, yeast cells were pelleted and resuspended in water. Approximately 500 cells/plate were spread on synthetic dextrose medium supplemented with uracil and all amino acids except arginine. Adenine was additionally present at 10 μg/ml, a limiting amount that allows red color development of Ade- cells. Plates were incubated at 30°C overnight and at room temperature for additional 2 days before being moved to 4°C to allow red pigment development.
Extracted molecule genomic DNA
Extraction protocol Cells in each half of a sectored colony were purified by streaking on YEP-glucose medium, and a single colony from each was used for DNA isolation. Genomic DNA was extracted in agarose plugs and then sheared to 200-400 bp by sonication.
Label Cy3
Label protocol DNA from each sector was labeled with Cy5-dUTP and mixed with control parental DNA labeled with Cy3-dUTP.
 
 
Hybridization protocol Mixed labeled DNA was competitively hybridized to a SNP microarray, and the ratio of Cy5 to Cy3 hybridization to each SNP was determined. Each SNP was represented by four 25-nt oligonucleotides that corresponded to the Watson and Crick strands of each homolog.
Scan protocol Scanned on an Agilent scanner (GenePix 4000B).
Description SJR4317 isolate#2 90-minute galactose induction, white sector9
Data processing The ratio of the medians (635 nm/532 nm) for each probe was used for analysis, and replicate probe medians were averaged (St. Charles et al., 2012).
 
Submission date Apr 28, 2017
Last update date Jan 23, 2018
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
 
Platform ID GPL21553
Series (1)
GSE98349 Mapping of mitotic gene conversion tracts associated with repair of a defined double-strand break (DSB) using SNP microarray

Data table header descriptions
ID_REF
VALUE normalized ratio Cy5/Cy3 representing DSB-induced sample/control

Data table
ID_REF VALUE
SF449787 1.075031169
YF449787 1.377178423
SF449974 1.109332911
SR449974 0.975045242
YF449974 0.912280354
YR449974 1.199101297
SF450125 1.08707327
SR450125 0.942932974
YF450125 0.975045242
YR450125 1.091087304
SF450218 0.709389203
SR450218 1.080139939
YF450218 0.680926056
YR450218 0.955339987
SF450596 1.512195915
YR450596 1.066273278
SF451249 1.317697743
SF451427 0.877248789
SR451427 0.936364555
YF451427 0.888196153

Total number of rows: 9213

Table truncated, full table size 180 Kbytes.




Supplementary file Size Download File type/resource
GSM2592555_9W.gpr.gz 1.5 Mb (ftp)(http) GPR
Processed data included within Sample table

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