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Sample GSM393202 Query DataSets for GSM393202
Status Public on Jul 08, 2010
Title SC (time 1) Replicate 3
Sample type RNA
 
Channel 1
Source name BY4741 time 1
Organism Saccharomyces cerevisiae
Characteristics test: BY4741
doubling time: 1
Treatment protocol Add fluconazole (4ug/mL for Sc and Cg, 0.06125ug/mL for Kl) at time 0
Growth protocol Grow samples at OD600 0.05 to 0.2. Treat half of sample with drug. Take samples at 0, 1/3, 2/3, 1, 2 and 4 doubling times (both treated and untreated).
Extracted molecule total RNA
Extraction protocol total RNA was extracted using hot phenol chloroform method. mRNA was isolated using Poly(A) purist kit (AM1916), Pool in equal amounts untreated samples for each replicate
Label Cy5
Label protocol Labeling performed using GE Healthcare Cyscribe First strand cDNA synthesis kit
 
Channel 2
Source name Reference Pool SC
Organism Saccharomyces cerevisiae
Characteristics reference: Reference Pool SC
Treatment protocol Add fluconazole (4ug/mL for Sc and Cg, 0.06125ug/mL for Kl) at time 0
Growth protocol Grow samples at OD600 0.05 to 0.2. Treat half of sample with drug. Take samples at 0, 1/3, 2/3, 1, 2 and 4 doubling times (both treated and untreated).
Extracted molecule total RNA
Extraction protocol total RNA was extracted using hot phenol chloroform method. mRNA was isolated using Poly(A) purist kit (AM1916), Pool in equal amounts untreated samples for each replicate
Label Cy3
Label protocol Labeling performed using GE Healthcare Cyscribe First strand cDNA synthesis kit
 
 
Hybridization protocol Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially
Scan protocol Arrays scanned using Genepix 4000A scanner and GenePix 6.0 software
Description dye swap replicate
Data processing Background subtraction and LOESS, missing values replaced by KNNimpute algorithm. Data was subsequently quantile normalized
 
Submission date Apr 16, 2009
Last update date Jul 08, 2010
Contact name Dwight Kuo
Organization name UCSD
Department Bioengineering
Lab Trey Ideker
Street address 9500 Gilman Dr.
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL7293
Series (1)
GSE15710 Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering (S. cerevisiae, C. glabrata, K. lactis)

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

Data table
ID_REF VALUE
A_06_P1001 -0.365521139
A_06_P1002 0.016855752
A_06_P1003 0.082874216
A_06_P1004 -1.568307269
A_06_P1005 -1.095174801
A_06_P1006 -1.516808089
A_06_P1007 -1.686772343
A_06_P1008 -0.766779012
A_06_P1009 -0.516333544
A_06_P1010 -0.499993892
A_06_P1011 -0.22921183
A_06_P1012 0.502027075
A_06_P1013 -0.170540254
A_06_P1014 1.773721111
A_06_P1015 1.278259431
A_06_P1016 -0.289458422
A_06_P1017 -0.41768958
A_06_P1018 -1.405195742
A_06_P1019 -0.853023346
A_06_P1020 -0.476731119

Total number of rows: 6255

Table truncated, full table size 142 Kbytes.




Supplementary file Size Download File type/resource
GSM393202.gpr.gz 1.1 Mb (ftp)(http) GPR
Processed data included within Sample table

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