|
| Status |
Public on Feb 10, 2007 |
| Title |
JW13-2 Aberration (898kb) |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
Reference strain genomic DNA
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
Reference strain genomic DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was prepared according to Lemoine et al 2005, Cell 120:587.
|
| Label |
Cy3
|
| Label protocol |
DNA was labelled according to Lemoine et al 2005, Cell 120:587.
|
| |
|
| Channel 2 |
| Source name |
JW13 898kb band DNA
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
DNA excised from CHEF gel.
|
| Extracted molecule |
other |
| Extraction protocol |
Agarose in CHEF gel slices was digested with beta-agarase I (New England Bioloabs) according to manufacturer recommendations. The DNA was then linearly amplified using the GenomiPhi DNA Amplification Kit (Amersham Biosciences) according to manufacturer recommendations. The DNA was then fragmented with a sonicator, concentrated with DNA Clean and Concentrator System (Zymo Research) and quantified in a spectrophotometer. Around 3ug of band-specific DNA were obtained using this protocol.
|
| Label |
Cy5
|
| Label protocol |
DNA was labelled according to Lemoine et al 2005, Cell 120:587.
|
| |
|
| |
| Hybridization protocol |
DNA was hybridized according to Lemoine et al 2005, Cell 120:587.
|
| Scan protocol |
Arrays were scanned with a GenePix 4000B scanner. Red and Green PMT gain were manually adjusted to about equal brightness in each channel. Pixel size was 10um and 2 lines were averaged.
|
| Description |
This array represents the hybridization of total genomic (Cy3) and DNA present in a specific region of a CHEF gel which was linearly amplified and labelled with Cy5.
|
| Data processing |
The data in the VALUE column was obtained by analyzing the data deposited at the University of North Carolina Microarray database (genome.unc.edu). The data from repeated spots in the array were collapsed to a single value per spot and centered according to the median. The VALUE corresponds to the Log2 RED/GREEN Normalized ratio based on the Median.
|
| |
|
| Submission date |
Feb 08, 2007 |
| Last update date |
Feb 09, 2007 |
| Contact name |
Juan Lucas Argueso |
| E-mail(s) |
lucas.argueso@duke.edu
|
| Phone |
1-919-684-5814
|
| Organization name |
Duke University Medical Center
|
| Department |
Molecular Genetics and Microbiology
|
| Street address |
371 CARL Building, Box 3054
|
| City |
Durham |
| State/province |
SP |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL4414 |
| Series (1) |
| GSE6991 |
Band-array detection of chromosomal rearrangements in diploid yeast cells exposed to ionizing radiation |
|
