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Sample GSM1274308 Query DataSets for GSM1274308
Status Public on Nov 28, 2013
Title gln-pro-alla-urea limited population
Sample type genomic
 
Channel 1
Source name Evolved population in gln-pro-alla-urea limited media
Organism Saccharomyces cerevisiae
Characteristics age: 250 generation
Treatment protocol All nitrogen-limiting media contained 800µM nitrogen regardless of the molecular form of the nitrogen and 1 g/L CaCl2-2H2O, 1 g/L of NaCl, 5 g/L of MgSO4-7H2O, 10 g/L KH2PO4, 2% glucose and trace metals and vitamins
Growth protocol Chemostat cultures were maintained for 250 generations using Sixfors fermentors (Infors) at 30°C, constantly stirred at 400 rpm in aerobic conditions and diluted at a rate of 0.12 hr-1 (population doubling time 5.8 hr).
Extracted molecule genomic DNA
Extraction protocol Genomic DNA (gDNA) from evolved clones and entire populations was prepared using the QIAGEN genomic DNA extraction kit
Label Cy3
Label protocol Sonicated DNA from each evolved clone or population was labeled with Cy3 and DNA from the ancestral strain was labeled with Cy5 using random hexamers and Klenow-mediated incorporation of label
 
Channel 2
Source name FY4 ancestor
Organism Saccharomyces cerevisiae
Characteristics age: 0 generataions
Treatment protocol All nitrogen-limiting media contained 800µM nitrogen regardless of the molecular form of the nitrogen and 1 g/L CaCl2-2H2O, 1 g/L of NaCl, 5 g/L of MgSO4-7H2O, 10 g/L KH2PO4, 2% glucose and trace metals and vitamins
Growth protocol Chemostat cultures were maintained for 250 generations using Sixfors fermentors (Infors) at 30°C, constantly stirred at 400 rpm in aerobic conditions and diluted at a rate of 0.12 hr-1 (population doubling time 5.8 hr).
Extracted molecule genomic DNA
Extraction protocol Genomic DNA (gDNA) from evolved clones and entire populations was prepared using the QIAGEN genomic DNA extraction kit
Label Cy5
Label protocol Sonicated DNA from each evolved clone or population was labeled with Cy3 and DNA from the ancestral strain was labeled with Cy5 using random hexamers and Klenow-mediated incorporation of label
 
 
Hybridization protocol Array Comparative Genomic Hybridization (aCGH) was performed using Agilent 60mer DNA microarrays. Hybridization reactions were performed at 65C for 17 hours after which microarrays were washed using the standard Agilent wash protocol.
Scan protocol Scanned on an Agilent Technologies Scanner G2505B
Description Evolved population in gln-pro-alla-urea limited media vs Ancestor (FY4) strain
Data processing DNA microarrays were analyzed using Agilent Feature Extractor. Data were normalized using a linear-loess normalization.
 
Submission date Nov 25, 2013
Last update date Nov 28, 2013
Contact name Jungeui Hong
E-mail(s) [email protected]
Organization name New York University
Department Biology
Lab Gresham Lab
Street address 12 Waverly Place
City New York
State/province NY
ZIP/Postal code 10003
Country USA
 
Platform ID GPL10930
Series (2)
GSE52696 Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments [aCGH]
GSE52787 Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments

Data table header descriptions
ID_REF
VALUE log2 ratio (Cy3/Cy5) of evolved/ancestor DNA copy number

Data table
ID_REF VALUE
A_75_P01108738 -0.09
A_75_P01407224 -0.03
A_75_P01701196 0.19
A_75_P02133858 0.06
A_75_P01755878 -0.22
A_75_P01936860 0.23
A_75_P01210286 0.2
A_75_P02068293 0.06
A_75_P01917499 -0.06
A_75_P01775070 -0.02
A_75_P01272067 -0.08
A_75_P01721250 0.06
A_75_P01102644 -0.1
A_75_P01434128 0.03
A_75_P01129739 0.05
A_75_P01981035 0.26
A_75_P02088155 0.27
A_75_P01843501 0.27
A_75_P01195408 -0.08
A_75_P01855545 0

Total number of rows: 41774

Table truncated, full table size 829 Kbytes.




Supplementary file Size Download File type/resource
GSM1274308_gln-pro-alla-urea_pop.txt.gz 13.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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