|
| Status |
Public on Feb 28, 2015 |
| Title |
Evolved Clone_1N_114 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Evolved Clone_1N
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: 1N_E3
sample type: Evolved Clone
|
| Treatment protocol |
The reference and progenitor strains were cultured in 5mL YPD overnight at 30C for genomic isolation. Single colony clones were isolated from the evolution experiment on SC+2% raffinose agar plates and grown up in 5mL SC+2% raffinose overnight at 30C for genomic isolation.
|
| Growth protocol |
The evolution experiment was performed in 1mL SC+2% Raffinose cultures in 96-well format at 30C with shaking.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard, phenol-chloroform genomic DNA preps were performed
|
| Label |
Cy3
|
| Label protocol |
Labeling was done as described previously (Selmecki et al 2005 Molecular Microbiology, and M. Dunham online protocols, http://dunham.gs.washington.edu/protocols.shtml). Briefly, 2.0 ug of HaeIII-digested (New England Biolabs) genomic DNA was labeled with 2.1 ul of Cy3 or Cy5 (CyDyeTm-Cy3-dUTP or CyDyeTm-Cy5-dUTP, Amersham GE Healthcare). 300 ng of Cy3-labeled DNA (all experimental strains) was mixed with 300 ng of Cy5-labeled DNA (reference control DNA) and the volume was brought to 44 ul with nuclease free water. Blocking Buffer and Hybridization Buffer 2x HiRPM (Agilent Technologies) were added, and 100 ul was applied to each sub-array; the microarray was hybridized at 65°C for 17 hours and then washed and scanned, according to the manufacturer’s instructions.
|
| |
|
| Channel 2 |
| Source name |
Reference Control_PY3295
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: PY3295
sample type: Reference Control
|
| Treatment protocol |
The reference and progenitor strains were cultured in 5mL YPD overnight at 30C for genomic isolation. Single colony clones were isolated from the evolution experiment on SC+2% raffinose agar plates and grown up in 5mL SC+2% raffinose overnight at 30C for genomic isolation.
|
| Growth protocol |
The evolution experiment was performed in 1mL SC+2% Raffinose cultures in 96-well format at 30C with shaking.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard, phenol-chloroform genomic DNA preps were performed
|
| Label |
Cy5
|
| Label protocol |
Labeling was done as described previously (Selmecki et al 2005 Molecular Microbiology, and M. Dunham online protocols, http://dunham.gs.washington.edu/protocols.shtml). Briefly, 2.0 ug of HaeIII-digested (New England Biolabs) genomic DNA was labeled with 2.1 ul of Cy3 or Cy5 (CyDyeTm-Cy3-dUTP or CyDyeTm-Cy5-dUTP, Amersham GE Healthcare). 300 ng of Cy3-labeled DNA (all experimental strains) was mixed with 300 ng of Cy5-labeled DNA (reference control DNA) and the volume was brought to 44 ul with nuclease free water. Blocking Buffer and Hybridization Buffer 2x HiRPM (Agilent Technologies) were added, and 100 ul was applied to each sub-array; the microarray was hybridized at 65°C for 17 hours and then washed and scanned, according to the manufacturer’s instructions.
|
| |
|
| |
| Hybridization protocol |
The microarray was hybridized at 65°C for 17 hours
|
| Scan protocol |
Default scan settings were used: Scan Area (61 x 21.6 mm), Scan resolution (5 um), Red & Green Dye channel, Green and Red PMT (100%)
|
| Description |
Evolved Clone vs WT DNA
|
| Data processing |
Agilent Feature Extraction (FE) analysis was performed
|
| |
|
| Submission date |
Sep 19, 2013 |
| Last update date |
Feb 28, 2015 |
| Contact name |
Anna Selmecki |
| E-mail(s) |
selme003@umn.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Lab |
Pellman
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL4131 |
| Series (1) |
| GSE51017 |
Polyploidy can drive rapid adaptation in yeast |
|
