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Sample GSM320583 Query DataSets for GSM320583
Status Public on Sep 16, 2008
Title Parental Yeast alpha-type Cell Replicate 1
Sample type genomic
 
Channel 1
Source name S. bayanus alpha-type cells
Organism Saccharomyces bayanus
Characteristics strain: S. bayanus#180
Growth protocol Yeast cells were grown in YPD medium, at 30 degree
Extracted molecule genomic DNA
Extraction protocol Yeast genomic DNA was extracted using QIAGEN Genomic-tip 100/G kit
Label Cy5
Label protocol fragmentation protocol:4.5 µg total genomic DNA were digested by 1 µl Dnase I (0.05 U) at 37 degree for 5 minutes and at 100 degree, 15 minutes for enzyme inactivation. The label protocol was adapted from Microarray Core Facility, Insititute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html)
 
Channel 2
Source name S. cerevisiae alpha-type cells
Organism Saccharomyces cerevisiae
Characteristics strain: W303
Growth protocol Yeast cells were grown in YPD medium, at 30 degree
Extracted molecule genomic DNA
Extraction protocol Yeast genomic DNA was extracted using QIAGEN Genomic-tip 100/G kit
Label Cy3
Label protocol fragmentation protocol:4.5 µg total genomic DNA were digested by 1 µl Dnase I (0.05 U) at 37 degree for 5 minutes and at 100 degree, 15 minutes for enzyme inactivation. The label protocol was adapted from Microarray Core Facility, Insititute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html)
 
 
Hybridization protocol The hybridization protocol was adapted from Microarray Core Facility, Insititute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html)
Scan protocol Arrays were scanned for F635(cy5) and F532(Cy3) fluoresence intensities using AXON 4000B ( Molecular Device , sunnyvale , CA )
Description The S. cerevisiae hybrid karyotypes were analyzed by array-CGH to identify small regions of duplication or homeologous chromosomal exchange occurring during the strain construction.
Data processing Subtracted background. Dividing by ch2 (control) was used to transform data (Agilent GeneSpring 7.3.1 software)
 
Submission date Sep 15, 2008
Last update date Sep 15, 2008
Contact name Jun-Yi Leu
E-mail(s) jleu@imb.sinica.edu.tw
Organization name Academia Sinica
Department Insititute of Molecular Biolody
Street address 128 Academia Road, Section 2, Nankang
City Taipei
ZIP/Postal code 115
Country Taiwan
 
Platform ID GPL7305
Series (2)
GSE12776 Karyotype analysis of S. cerevisiae chromosome replacement lines - alpha-type cells
GSE12785 Karyotype analysis of S. cerevisiae chromosome replacement lines

Data table header descriptions
ID_REF
VALUE log ch1/ch2
ch1
ch2
RATIO ch1/ch2

Data table
ID_REF VALUE ch1 ch2 RATIO
1 -2.5850 2 12 0.16666666
2 -4.8365 154 4400 0.035
3 -6.0669 128 8581 0.014916675
4 -0.2944 5606 6875 0.8154182
5 -5.4195 183 7832 0.023365682
6 -5.3404 242 9805 0.024681285
7 -5.2885 143 5589 0.02558597
8 -4.8034 374 10443 0.03581346
9 -0.5481 3642 5325 0.6839437
10 -1.6966 2060 6677 0.30852178
11 -0.3313 6322 7954 0.7948202
12 -0.6329 1669 2588 0.64489955
13 -5.8428 74 4247 0.017424066
14 -0.1113 7818 8445 0.9257549
15 -2.1636 2785 12478 0.22319284
16 -3.8961 512 7623 0.06716516
17 -5.6753 287 14666 0.019569071
18 -0.9236 7938 15057 0.52719665
19 -1.3236 3016 7549 0.3995231
20 -5.7216 125 6596 0.01895088

Total number of rows: 6400

Table truncated, full table size 200 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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