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Sample GSM3329624 Query DataSets for GSM3329624
Status Public on Aug 11, 2018
Title HO-0.5-21R
Sample type genomic
 
Channel 1
Source name cell culture of strain HO-0.5-21R
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) zhengdaoqiong@163.com
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 GPL21553
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
SF1000365 0.921134649
SF1001602 null
SF1002104 1.310410225
SF1002163 null
SF1002452 1.339832216
SF1003678 1.082955601
SF1003797 1.135009893
SF1003836 null
SF1003935 0.726496861
SF1004465 1.045612304
SF1005641 null
SF1006070 1.106719517
SF1006514 1.211959716
SF1007002 1.040520036
SF1007144 1.393018124
SF1007582 1.089179483
SF1008785 null
SF1008829 1.08069237
SF1008881 null
SF1009116 0.964701828

Total number of rows: 9213

Table truncated, full table size 177 Kbytes.




Supplementary file Size Download File type/resource
GSM3329624_HO-0.5-21R.gpr.gz 1.6 Mb (ftp)(http) GPR
Processed data included within Sample table

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