NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3329738 Query DataSets for GSM3329738
Status Public on Aug 11, 2018
Title HO-0.5-19R
Sample type genomic
 
Channel 1
Source name cell culture of strain HO-0.5-19R
Organism Saccharomyces cerevisiae
Characteristics ploidy: diploid strain
strain: W303-1AxYJM789
Treatment protocol JSC25 cells were grown in 7 mL YPD overnight to reach an OD600 of 0.2. Yeast cells (5×107) were collected by centrifugation and arrested in G1 in 1 mL YPD containing 2.5 μg α-factor at 30 degree. After two hours, H2O2 was added into the cell culture. Cell culture was incubated at 30 degree for another hour. Yeast cells were then washed twice to remove α-factor and H2O2 before plating. Yeast cells were cultured at 30 degree for 3 days and sectored colonies were selected for chromosome IV SNP-specific microarrays.
Growth protocol Yeast cells were grown in YPD medium at 30 degree.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA were prepared by standard procedures (St. Charles et al., 2012)
Label cy5
Label protocol DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain JSC24) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.
 
Channel 2
Source name cell culture of JSC24
Organism Saccharomyces cerevisiae
Characteristics strain: control strain JSC24
ploidy: diploid strain
Treatment protocol JSC25 cells were grown in 7 mL YPD overnight to reach an OD600 of 0.2. Yeast cells (5×107) were collected by centrifugation and arrested in G1 in 1 mL YPD containing 2.5 μg α-factor at 30 degree. After two hours, H2O2 was added into the cell culture. Cell culture was incubated at 30 degree for another hour. Yeast cells were then washed twice to remove α-factor and H2O2 before plating. Yeast cells were cultured at 30 degree for 3 days and sectored colonies were selected for chromosome IV SNP-specific microarrays.
Growth protocol Yeast cells were grown in YPD medium at 30 degree.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA were prepared by standard procedures (St. Charles et al., 2012)
Label Cy3
Label protocol DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain JSC24) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.
 
 
Hybridization protocol The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.
Scan protocol The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.
Data processing The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio. The Whole genome arrays were completed with Agilent platform with Design ID Agilent-027438 was used. Sectored colonies were mapped using Agilent platforsm with Design IDs Agilent-031671, which contains probes specific only to chromosome IV, and Agilent-047217, which contains many probes on chromsome IV, but few probes near the telomere and centromere of all chromosomes.
 
Submission date Aug 10, 2018
Last update date Aug 11, 2018
Contact name Daoqiong Zheng
E-mail(s) [email protected]
Phone 86 571 88206636
Organization name College of Life Sciences, Zhejiang University
Department Institute of Microbiology
Street address 866 Yuhangtang Road
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310058
Country China
 
Platform ID GPL21552
Series (1)
GSE106816 Effects of oxidative stress on mitotic recombination and genomic stability in yeast

Data table header descriptions
ID_REF
VALUE Ratio of the medians (635 nm/532 nm).

Data table
ID_REF VALUE
j2chr1:11096SF 0.425203021
j2chr1:11096SR 1.120690134
j2chr1:11096YF 0.648517011
j2chr1:11096YR 1.072895996
j2chr1:127399SR 0.942698171
j2chr1:127399YF 1.249239885
j2chr1:127399YR 1.043230669
j2chr1:148136SF 0.852054116
j2chr1:148136SR 0.828981084
j2chr1:148136YF 0.777066762
j2chr1:148136YR 0.624619942
j2chr1:152326SF 1.063007553
j2chr1:152326SR 0.786131167
j2chr1:152326YF 1.184965009
j2chr1:152326YR 1.100913249
j2chr1:153172SF 1.06135948
j2chr1:153172SR 0.865238706
j2chr1:153172YF 1.374493488
j2chr1:153172YR 0.873479075
j2chr1:159612SF 0.848757969

Total number of rows: 12240

Table truncated, full table size 276 Kbytes.




Supplementary file Size Download File type/resource
GSM3329738_HO-0.5-19R.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