|
| Status |
Public on Apr 03, 2015 |
| Title |
Day 2 Control Replicate C vs. Box A Day 30 Replicate C |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Whole bodies of Drosophila melanogaster females
|
| Organism |
Drosophila melanogaster |
| Characteristics |
population: Outbred population
day: 2
replicate: C
box: A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Indirect labeling with Cy3/Cy5 fluorescent dyes was performed using 12 ug of total RNA per sample using the Superscript Indirect cDNA Labeling System for DNA microarrays.
|
| |
|
| Channel 2 |
| Source name |
Whole bodies of Drosophila melanogaster females
|
| Organism |
Drosophila melanogaster |
| Characteristics |
population: Outbred population
day: 30
replicate: C
box: A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
Indirect labeling with Cy3/Cy5 fluorescent dyes was performed using 12 ug of total RNA per sample using the Superscript Indirect cDNA Labeling System for DNA microarrays.
|
| |
|
| |
| Hybridization protocol |
Prior to hybridization, the microarray slides were pre-hybridized for 45 minutes at 42°C in 3X SSC solution (3 M NaCl, 0.3 M sodium citrate, 1 mM EDTA) containing 1% bovine serum albumin. The Cy3 and Cy5 probes were mixed together in 40 ul Ambion hybridization buffer #2 (Ambion). Blocking agents that included poly-dA (20 ug) and Cot-1 DNA (20 ug) were added. Hybridization was performed overnight at 42°C. After hybridization, the slides were washed 2x times with 2.0x SSC, 0.5% SDS at 42 degrees for 15 minutes, followed by washing 2x with 0.5x SSC, 0.50% SDS for 15 minutes each.
|
| Scan protocol |
Cy3 (532 nm) and Cy5 (635 nm) scans were performed using an ScanPix 4000B slide reader per manufacturer’s suggested conditions (Molecular Devices, Sunnyvale, CA).
|
| Description |
Biological replicate C. Collected after 2 days of being in the box vs. Box A Control Replicate C, which was collected after 30 days of being in the box.
|
| Data processing |
Following image capture, the overall images, as well as the individual spots, were assessed for uniformity of hybridization and individual integrity. Problematic spots (i.e. bad morphology or those with aberrant hybridization properties) were flagged for subsequent removal from the final data set. The intensity assessment for gene spots from 16 bit TIFF files was performed with the GenePix image analysis software (Molecular Devices).
|
| |
|
| Submission date |
Apr 02, 2015 |
| Last update date |
Apr 03, 2015 |
| Contact name |
Kimberly Ann Carlson |
| E-mail(s) |
carlsonka1@unk.edu
|
| Phone |
308-865-1554
|
| Organization name |
University of Nebraska at Kearney
|
| Department |
Biology
|
| Street address |
2401 11th Ave, BHS 300
|
| City |
Kearney |
| State/province |
NE |
| ZIP/Postal code |
68849 |
| Country |
USA |
| |
|
| Platform ID |
GPL19987 |
| Series (1) |
| GSE67547 |
Microarray analysis of large caged once mated females mortality study |
|
