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Sample GSM4050916 Query DataSets for GSM4050916
Status Public on Dec 31, 2020
Title sk1vsby4743-1
Sample type genomic
 
Channel 1
Source name SK1
Organism Saccharomyces cerevisiae
Characteristics strain: SK1
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 laboratory
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-sensitive 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 -0.972
Q0017 -0.833
Q0032 0.408
Q0045 0.448
Q0050 0.675
Q0055 -3.296
Q0060 -0.15
Q0065 0.46
Q0070 -5.109
Q0075 0.71
Q0080 1.1
Q0085 0.635
Q0092 -0.068
Q0105 0.406
Q0110 -3.311
Q0115 0.6
Q0120 0.772
Q0130 0.835
Q0140 1.384
Q0142 1.037

Total number of rows: 6317

Table truncated, full table size 88 Kbytes.




Supplementary file Size Download File type/resource
GSM4050916_sk1vsby4743-1.gpr.gz 472.9 Kb (ftp)(http) GPR
Processed data included within Sample table

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