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Sample GSM5968382 Query DataSets for GSM5968382
Status Public on Mar 26, 2022
Title Cross of MD893-1 with LSY3454-2 Zygote4
Sample type genomic
 
Channel 1
Source name cell culture of strain MD891_4
Organism Saccharomyces cerevisiae
Characteristics type: diploid strain
strain: W303-1AⅹYJM789
Treatment protocol Isolates were grown in liquid YPD medium and the genomic DNA from independent isolates was extracted and analyzed by the whole-genome microarrays.
Growth protocol Yeast cells were grown 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
type: diploid strain
Treatment protocol Isolates were grown in liquid YPD medium and the genomic DNA from independent isolates was extracted and analyzed by the whole-genome microarrays.
Growth protocol Yeast cells were grown 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.
Processed data: Ratio of the medians (635 nm/532 nm).
 
Submission date Mar 23, 2022
Last update date Mar 27, 2022
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)
GSE199262 Ribodysgenesis: sudden genome instability in the yeast Saccharomyces cerevisiae arising from RNase H2 cleavage at genomic-embedded ribonucleotides

Supplementary file Size Download File type/resource
GSM5968382_MD891_4.gpr.gz 10.3 Mb (ftp)(http) GPR
Processed data are available on Series record

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