|
| Status |
Public on Jun 26, 2013 |
| Title |
Pupae at LDC (6g) constrained (↓O2), biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Drosophila pupae before imagoes hatch
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: late pupae
strain: Oregon R
age: late pupae just before eclosion
g level: 6g
environment (Δt): normal
environment (↓o2): suboptimal
magnetic field (*): No
|
| Treatment protocol |
Early pupae were exposed to a cold step (ΔT) previous to the gravitational treatment or not. During the gravitational treatment pupae have a limite amount of oxigen (↓O2) in a closed container or not. Flies were exposed to different altered gravity simulators (RPM, Magnetic levitator, centrifgue) and inmediately after the treatment were placed on ice in the Trizol solution (GibcoBRL).
|
| Growth protocol |
OreR late larvae were developed at 24C during 3.5 days into different gravitational and environmental conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using GeneChip® Scanner 3000 7G System
|
| Description |
DmPupae_Q8H.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis
|
| Data processing |
Analysis was performed using FIESTA viewer (bioinfogp.cnb.csic.es/tools/FIESTA). Robust Multi-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization (Irizarry et al., 2003). Next, differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (limma). P-values were corrected for multiple-testing using the Benjamini-Hochberg’s method (False Discovery Rate) (Benjamini and Hochberg, 1995; Reiner et al., 2003).
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| |
|
| Submission date |
Nov 17, 2011 |
| Last update date |
Jun 26, 2013 |
| Contact name |
Raúl Herranz |
| E-mail(s) |
r.herranz@csic.es
|
| Phone |
+34918373112
|
| Fax |
+34915360432
|
| Organization name |
Centro Investigaciones Biológicas
|
| Department |
Plant Cell Nucleolus, proliferation and microgravity
|
| Lab |
Lab.205
|
| Street address |
Ramiro de Maeztu 9
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28040 |
| Country |
Spain |
| |
|
| Platform ID |
GPL1322 |
| Series (2) |
| GSE33779 |
Environmental and facility conditions promote singular gravity responses of transcriptome during Drosophila metamorphosis |
| GSE33803 |
Environmental and simulation facility conditions can modulate gravity response of Drosophila transcriptome |
|
