|
| Status |
Public on Oct 11, 2010 |
| Title |
control_2nd_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
whole larvae, control, 2nd instar
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: whole larva
larval stage: 2
genotype/variation: U6atac/CyO-GFP (control)
|
| Treatment protocol |
1st stage larvae were collected from apple juice agar plates, 2nd and 3rd stage larvae from fly food vials.
|
| Growth protocol |
Flies were grown on standard food at 25 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from larvae with Trizol reagent (Invitrogen).
|
| Label |
Cy5
|
| Label protocol |
1 μg of each RNA sample was amplified with Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion/Applied Biosystems) according to manufacturer's instructions. In vitro transcription reaction was incubated for 8 hours. The resulting aminoallyl-modified RNA was labelled with Cy3 or Cy5 dyes (Invitrogen) or ARES Labeling Kit with Alexa Fluor 488 (Invitrogen).
|
| |
|
| Hybridization protocol |
0.75 μg of each three samples per array were hybridized with Gene Expression Hybridization Kit (Agilent) according to the protocol for Two-Color Microarray-Based Gene Expression Analysis.
|
| Scan protocol |
The arrays were scanned with Genepix 4200A scanner and Genepix Pro 6.1.0.2 software.
|
| Description |
GFP2_s1a1_635
raw data file: slide001_A1_635GFP2_532-U6a3_0489.gpr
|
| Data processing |
The gpr files were imported into R 2.9.0 (cran.r-project.org) and analyzed with the BioConductor (www.bioconductor.org) package Limma. The median foreground probe intensities without background correction from each channel were log2 transformed and normalized by the quantile method. Exon-exon junction probes were excluded from the analysis due to unreliability.
Exon-level data reported in the Data table below.
|
| |
|
| Submission date |
Sep 15, 2010 |
| Last update date |
Oct 07, 2010 |
| Contact name |
Heli Pessa |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Helsinki
|
| Department |
Faculty of Medicine; Research Programme in Translational Immunology
|
| Lab |
Saavalainen
|
| Street address |
Haartmaninkatu 8
|
| City |
Helsinki |
| ZIP/Postal code |
00014 |
| Country |
Finland |
| |
|
| Platform ID |
GPL10915 |
| Series (1) |
|
