|
| Status |
Public on Mar 01, 2010 |
| Title |
TT MF CGH replicate 3 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Total DNA from four flies, labeled with Cyanine-5 (red).
|
| Organism |
Teleopsis thaii |
| Characteristics |
sex: female
age: adult
tissue: whole fly
population: Chiang Mai
|
| Growth protocol |
Each sample consisted of 4 or 5 male or female adult flies that were taken from population cages maintained at the University of Maryland, College Park, derived from flies originally collected from SE Asia
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from macerated fly bodies with Qiagen DNeasy kits using the insect sample protocol
|
| Label |
Cy5
|
| Label protocol |
Each DNA sample was fractionated by restriction digestion with AluI and RsaI for 2 h at 37oC. 3 µg of each sample was then labeled with either Cy-3 or Cy-5
|
| |
|
| Channel 2 |
| Source name |
Total DNA from four flies, labeled with Cyanine-3 (green).
|
| Organism |
Teleopsis thaii |
| Characteristics |
sex: male
age: adult
tissue: whole fly
population: Chiang Mai
|
| Growth protocol |
Each sample consisted of 4 or 5 male or female adult flies that were taken from population cages maintained at the University of Maryland, College Park, derived from flies originally collected from SE Asia
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from macerated fly bodies with Qiagen DNeasy kits using the insect sample protocol
|
| Label |
Cy3
|
| Label protocol |
Each DNA sample was fractionated by restriction digestion with AluI and RsaI for 2 h at 37oC. 3 µg of each sample was then labeled with either Cy-3 or Cy-5
|
| |
|
| |
| Hybridization protocol |
Agilent array-based CGH protocol with hybridization for 24 h at 65oC
|
| Scan protocol |
Scanned using an Agilent G2539A microarray scanner
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
|
| Description |
Biological replicate 3 of 4
|
| Data processing |
Agilent Feature Extraction Software (v 8.5.1.1) was used. Features were excluded from further analysis if the majority of pixels were saturated or the median pixel intensity was less than two times the background. Intensity scores were normalized using the linear normalization methodology. Data included in the Matrix table differ from the LogRatio column in the Agilent Feature Extraction Files in that each sample has been normalized. The order of data manipulation was 1) probes normalized by agilent software, 2) median probe value for each ORF calculated, 3) median value of logratio(F/M) centralized so peak above 0
|
| |
|
| Submission date |
Feb 12, 2010 |
| Last update date |
Feb 12, 2010 |
| Contact name |
Gerald S Wilkinson |
| E-mail(s) |
wilkinso@umd.edu
|
| Phone |
301-405-6942
|
| Organization name |
University of Maryland
|
| Department |
Biology
|
| Lab |
Wilkinson
|
| Street address |
Bldg 144, 4094 Campus Dr
|
| City |
College Park |
| State/province |
MD |
| ZIP/Postal code |
20742 |
| Country |
USA |
| |
|
| Platform ID |
GPL10043 |
| Series (1) |
| GSE20315 |
CGH reveals a neo-X chromosome and biased gene movement in stalk-eyed flies (genus Teleopsis) |
|
