|
| Status |
Public on Oct 07, 2009 |
| Title |
pCs41scpr20060510_melM3yakM5_67_opt |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Drosophila melanogaster
|
| Organism |
Drosophila melanogaster |
| Characteristics |
gender: male
species: melanogaster
|
| Biomaterial provider |
Tucson Drosophila Stock Center
|
| Treatment protocol |
none
|
| Growth protocol |
Grown in fly nutrient media
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ProteinaseK/Phenol Extraction
|
| Label |
Cy3
|
| Label protocol |
dCTP incorporation with Klenow
|
| |
|
| Channel 2 |
| Source name |
Drosophila yakuba
|
| Organism |
Drosophila yakuba |
| Characteristics |
gender: female
species: yakuba
|
| Biomaterial provider |
Tucson Drosophila Stock Center
|
| Treatment protocol |
none
|
| Growth protocol |
Grown in fly nutrient media
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ProteinaseK/Phenol Extraction
|
| Label |
Cy5
|
| Label protocol |
dCTP incorporation with Klenow
|
| |
|
| |
| Hybridization protocol |
The samples were combined with hybridization buffer (3.4X SSC, 0.15% SDS, 1 mM DTT) and hybridized to the microarray at 67 degrees 12-16 hours
|
| Scan protocol |
Fluorescent array images were collected for both Cy3 and Cy5 with an Axon 4000B scanner adjusting the intensities to be roughly balance. Images filtered for bad spot morphology in Genepix 5.0.
PMTGain=840_720 ScanPower=100_100
|
| Description |
Cy3= male_melanogaster genomic DNA Cy5= female_yakuba genomic DNA hybed by SCP Renn on 2004
|
| Data processing |
After removing ""flagged"" and bad spots, only those spots were used whose average intensity was at least two standard deviations above the average background. Arrays were background corrected (method minimal) and normalized in R/Bioconductor with within-arrays loess (using a set of 1000 conserved genes) and intensity ratios were calculated.
|
| |
|
| Submission date |
Oct 05, 2009 |
| Last update date |
Oct 06, 2009 |
| Contact name |
Suzy C.P. Renn |
| E-mail(s) |
renns@reed.edu
|
| Phone |
503 517 7967
|
| Organization name |
Reed College
|
| Department |
Biology
|
| Street address |
3203 SE Woodstock Blvd
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97202 |
| Country |
USA |
| |
|
| Platform ID |
GPL6056 |
| Series (1) |
|
| Data table header descriptions |
| ID_REF |
|
| F635 Median |
635nm Foreground intensity Median |
| F635 Mean |
635nm Foreground intensity Mean |
| F635 SD |
635nm Foreground intensity Standard Deviation |
| B635 Median |
635nm Background intensity Median |
| B635 Mean |
635nm Background intensity Mean |
| B635 SD |
635nm Background intensity Standard Deviation |
| F532 Median |
532nm Foreground intensity Median |
| F532 Mean |
532nm Foreground intensity Mean |
| F532 SD |
532nm Foreground intensity Standard Deviation |
| B532 Median |
532nm Background intensity Median |
| B532 Mean |
532nm Background intensity Mean |
| B532 SD |
532nm Background intensity Standard Deviation |
| Flags |
Feature Flags: both automated and mannually applied |
| VALUE |
log2 ratio normalized (Cy5/Cy3) |
