NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2079732 Query DataSets for GSM2079732
Status Public on Mar 03, 2016
Title DZ12-sectored-Red27 (S51R)
Sample type genomic
 
Channel 1
Source name DZ12-derived sectored colonies
Organism Saccharomyces cerevisiae
Characteristics ploidy: Diploid
background: W3031-AxYJM789
strain: diploid strain DZ12
growth protocol: YPD medium
Treatment protocol The expression of POL3 were downregulated using either low-gal medium or YPD medium.
Growth protocol Yeast cells were cultured in low-gal (2% yeast extract, 2% peptone and 3% raffinose, 0.005% galactose) or high-gal medium (2% yeast extract, 2% peptone and 3% raffinose, 0.05% galactose) to extract DNA
Extracted molecule genomic DNA
Extraction protocol Genomic DNA were prepared DNA by standard procedures (St. Charles et al., 2012).
Label Cy5
Label protocol The description of the labeling and hybridization protocol are copied with minor modifications from the Supplementary Information of our previous publication: 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 Control strain JSC24
Organism Saccharomyces cerevisiae
Characteristics ploidy: Diploid
background: W303-1AxYJM789
strain: control strain JSC24
Treatment protocol The expression of POL3 were downregulated using either low-gal medium or YPD medium.
Growth protocol Yeast cells were cultured in low-gal (2% yeast extract, 2% peptone and 3% raffinose, 0.005% galactose) or high-gal medium (2% yeast extract, 2% peptone and 3% raffinose, 0.05% galactose) to extract DNA
Extracted molecule genomic DNA
Extraction protocol Genomic DNA were prepared DNA by standard procedures (St. Charles et al., 2012).
Label Cy3
Label protocol The description of the labeling and hybridization protocol are copied with minor modifications from the Supplementary Information of our previous publication: 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.
Description DZ12-derived Red sectored colonies
Data processing The ratio of the medians (635 nm/532 nm) for each probe was used for analysis, and replicate probe medians were averaged. The data was centered around one by dividing each probe median by the average of all of the probe medians in order to normalize for differences in the hybridization levels for the reference and experimental strain samples. The data were plotted separately for each haploid parental strain and, in plots showing whole chromosomes, the medians were “smoothed” by averaging over nine consecutive probes. In the labels of the oligonucleotides “SF”, “SR”, “YF” and “YR” refer to the orientation and origin of the sequences used for the oligonucleotides on the microarrays. “S” and “Y” indicate whether the oligonucleotide contains sequences identical to the reference S288c genome (closely related to W303-1A) or the YJM789 genome, respectively. “F” and “R” indicate whether the orientation (5’ to 3’) is identical to the orientation in SGD (“F” standing for forward) or opposite to that shown in SGD (“R” for reverse). Thus, “F” and “R” have the sequences of the complementary Watson and Crick strands at each position. For all oligonucleotides for a particular SNP, the number used to label the coordinate is the coordinate of the first base of the oligonucleotide in the “F” orientation. In addition, the oligonucleotides for the YJM789-derived sequences were labeled with the same coordinate as the S288c-derived sequences. The sequence information for the YJM789 sequences was from SGD based on the paper by (Wei et al., 2007. PNAS 104:12825-12830). 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 Mar 03, 2016
Last update date Mar 03, 2016
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)
GSE78856 Genomic instability induced by lowered expression of POL3 in yeast

Data table header descriptions
ID_REF
VALUE Normalized ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
SF1000365 1.01621877818434
SF1001602 0.704398888189589
SF1002104 1.45590725616256
SF1002163 0.580269147807984
SF1002452 0.883115803558286
SF1003678 0.949667290871315
SF1003797 1.45515948664219
SF1003836 1.25326171614199
SF1003935 1.14782621376966
SF1004465 1.1313752843215
SF1005641 0.854700561784183
SF1006070 0.803104464878576
SF1006514 1.02369647338805
SF1007002 1.25101840758087
SF1007144 1.3280386681791
SF1007582 0.924990896699068
SF1008785 0.544376210830171
SF1008829 1.00500223537878
SF1008881 0.801608925837834
SF1009116 0.989299075450984

Total number of rows: 8204

Table truncated, full table size 215 Kbytes.




Supplementary file Size Download File type/resource
GSM2079732_S51R.analysed.txt.gz 95.2 Kb (ftp)(http) TXT
GSM2079732_S51R.gpr.gz 1.5 Mb (ftp)(http) GPR
Processed data provided as supplementary file
Processed data included within Sample table

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