NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4050907 Query DataSets for GSM4050907
Status Public on Dec 31, 2020
Title SG60vsby4743-2
Sample type genomic
 
Channel 1
Source name SG60
Organism Saccharomyces cerevisiae
Characteristics strain: SG60
Growth protocol strains were grown in YPD (1% Yeast Extract, 2% Peptone, 2% glucose) overnight at 30€™C in shaking.
Extracted molecule genomic DNA
Extraction protocol genomic DNA was extracted from over-night strains cultures with the phenol-chloroform protocol. DNA quality was checked through gel electrophoresis and photometric measurement.
Label Cy5
Label protocol The genomic DNA extracted was concentrated using the filter Microcon YM-30 (Millipore) and fragmented by sonication. The labeling of the DNA was performed, at 37°C for 2 hours, using the BioPrime DNA labeling Sytem (Invitrogen, Life Technologies), but using 100mM dNTP set (Invitrogen, Life Technologies) instead of the biotinilated nucleotides present in the kit, as well as the fluorescent nucleotides Cy3-dCTP and Cy5-dCTP of Amersham, GE Healthcare. Once finished the reaction, the DNA was purified with the Microcon YM-30 and the appropriate pairs of samples labeled with the different fluorochromes were combined in a single eppendorf in 450µL of TE (Tris-EDTA), pH 8.0 (Sigma-Aldrich). We used Human cot-1 DNA (Invitrogen, Life Technologies) to block non-specific hybridization, and Yeast tRNA (Invitrogen, Life Technologies) as coprecipitant.
 
Channel 2
Source name Wine grape
Organism Saccharomyces cerevisiae
Characteristics strain: BY4743
Growth protocol strains were grown in YPD (1% Yeast Extract, 2% Peptone, 2% glucose) overnight at 30€™C in shaking.
Extracted molecule genomic DNA
Extraction protocol genomic DNA was extracted from over-night strains cultures with the phenol-chloroform protocol. DNA quality was checked through gel electrophoresis and photometric measurement.
Label Cy3
Label protocol The genomic DNA extracted was concentrated using the filter Microcon YM-30 (Millipore) and fragmented by sonication. The labeling of the DNA was performed, at 37°C for 2 hours, using the BioPrime DNA labeling Sytem (Invitrogen, Life Technologies), but using 100mM dNTP set (Invitrogen, Life Technologies) instead of the biotinilated nucleotides present in the kit, as well as the fluorescent nucleotides Cy3-dCTP and Cy5-dCTP of Amersham, GE Healthcare. Once finished the reaction, the DNA was purified with the Microcon YM-30 and the appropriate pairs of samples labeled with the different fluorochromes were combined in a single eppendorf in 450µL of TE (Tris-EDTA), pH 8.0 (Sigma-Aldrich). We used Human cot-1 DNA (Invitrogen, Life Technologies) to block non-specific hybridization, and Yeast tRNA (Invitrogen, Life Technologies) as coprecipitant.
 
 
Hybridization protocol Hybridization took place at 65 °C for 16 h.
Scan protocol Fluorescent DNA bound to the microarray was detected with a GenePix 4000B microarray scanner (Axon Instruments), using the GenePixPro6.1 software package to quantify microarray fluorescence.
Description Arsenic-resistant strain
Data processing Data were normalized using the limma R package and DEGs (Differentially Expressed Genes) were identified with the RankProduct R package
 
Submission date Aug 27, 2019
Last update date Jan 01, 2021
Contact name Irene Stefanini
E-mail(s) stefanini.irene@gmail.com
Organization name University of Turin
Street address via Accademia Albertina
City Torino
ZIP/Postal code 10123
Country Italy
 
Platform ID GPL27156
Series (1)
GSE136466 CGH of natural Saccharomyces cerevisiae strains

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
Q0010 -0.032
Q0017 0.026
Q0032 -1.204
Q0045 0.739
Q0050 -4.396
Q0055 0.977
Q0060 -4.957
Q0065 0.956
Q0070 -7.444
Q0075 0.994
Q0080 2.143
Q0085 0.889
Q0092 -0.496
Q0105 1.081
Q0110 0.179
Q0115 0.567
Q0120 0.681
Q0130 0.855
Q0140 1.168
Q0142 0.443

Total number of rows: 6317

Table truncated, full table size 89 Kbytes.




Supplementary file Size Download File type/resource
GSM4050907_SG60vsby4743-2.gpr.gz 558.8 Kb (ftp)(http) GPR
Processed data included within Sample table

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