|
| Status |
Public on Nov 28, 2013 |
| Title |
arginine limited population |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Evolved population in arginine 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 arginine 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) |
jh2663@nyu.edu
|
| 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 |
|
