|
| Status |
Public on May 31, 2013 |
| Title |
line5, subline +D, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
line5_most depressed subline
|
| Organism |
Drosophila melanogaster |
| Characteristics |
origin: Vigo (NW Spain)
line: most depressed inbred subline from line 5
age/gender: adult male
tissue: whole body
|
| Treatment protocol |
From a large outbred base population we sampled four couples to found four inbred lines. From each initial couple, 55 inbred sublines were established and maintained for 8 generations of sib mating with the objective of fixing in different sublines the genetic variation segregating in the initial couple. Single pair mating was carried out until generation 4, but two males and two females were mated per vial thereafter, to avoid further subline losses. The final average inbreeding coefficient was about 0.7.
|
| Growth protocol |
Flies were reared in a culture medium composed of 1 liter water, 100 g brewer’s yeast, 100 g sucrose, 12 g agar, 2.5 g NaCl, and 5 ml propionic acid and were handled at room temperature under CO2 anesthesia. All cultures were incubated in a chamber at 25 6 1_, 65 6 5% relative humidity, and maintained under continuous lighting. Virgin males and females were used for mating across the entire experiment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was performed with RNeasy Mini kit (QIAGEN, Valencia, CA)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, Affymetrix).
|
| |
|
| Hybridization protocol |
15 mg of each biotinylated cRNA sample were fragmented and mixed with hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween 20) using Affymetrix fluidic station
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Description |
09SE003
|
| Data processing |
The robust multichip average (RMA) method was used for background adjustment, quantile normalization, and probe-level summarization of the microarray samples. RMA expression summary was computed using Partek Genomics Suite v. 7.3.3 (Partek) and the affy package in Bioconductor (v.1.18.2).
Normalized data for Drosophila expression patterns including inbred lines (N = 24) and the outbred controls (N = 3) are provided in the sample data table.
Normalized data matrix of Drosophila expression patterns including only inbred lines (N = 24) is provided as Series supplementary file (inbred_only_data.txt)
|
| |
|
| Submission date |
May 22, 2013 |
| Last update date |
May 31, 2013 |
| Contact name |
Humberto Quesada |
| E-mail(s) |
[email protected]
|
| Organization name |
Universidad de Vigo
|
| Department |
Bioquimica, Genetica e Inmunologia
|
| Lab |
Genetics
|
| Street address |
Facultad de Biologia. Campus Lagoas-Marcosende
|
| City |
Vigo |
| State/province |
Galicia |
| ZIP/Postal code |
36310 |
| Country |
Spain |
| |
|
| Platform ID |
GPL1322 |
| Series (1) |
| GSE47176 |
Candidate transcriptomic sources of inbreeding depression in Drosophila melanogaster |
|
