|
| Status |
Public on Oct 01, 2011 |
| Title |
D. montana whole body 19C control rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Whole body pool of the flies control rep2
|
| Organism |
Drosophila montana |
| Characteristics |
gender: female
developmental stage: mature
age: 20 d
treatment: Whole body 19C control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Three pools of ten flies per sample were grounded and transferred into 1.5 ml tubes and mixed with 600 µl of lysis buffer. The total RNA was extracted using Qiagen RNA extraction kit with RNase-Free DNase treatment according to manufacturer's protocols (QIAGEN, Hilden, Germany). The purity of each RNA sample was measured with NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and the integrity of the samples was studied with Agilent’s Bioanalyzer (Agilent, Santa Clara, CA, USA).
|
| Label |
Cy3
|
| Label protocol |
600 ng of total RNA from each replicate was amplified and Cy3-labeled with Agilent’s Quick Amp Labeling (One Color) Kit and processed together with Agilent’s One-Colour RNA Spike-in Kit.
|
| |
|
| Hybridization protocol |
600 ng of each cRNA sample was hybridized to Agilent’s 8x15K D. montana / D. virilis custom arrays at 65˚C. Hybridization was performed overnight using Agilent’s Gene Expression Hybridization Kit and the plates were washed with Agilent’s Gene Expression Wash Pack and Stabilization and Drying solution.
|
| Scan protocol |
Arrays were scanned with Agilent Technologies Scanner (model G2565CA) and numerical results were extracted with Feature Extraction software version 10.7.1 using 026691_D_F_20091221grid, GE1_107_Sep09 protocol and GE1_QCMT_Sep09 metric set.
|
| Data processing |
The downstream analysis of the microarray data was carried out using R (R Foundation for Statistical Computing) and Bioconductor software (Gentleman et al., 2004). Probe level quantile normalization method was used for between sample normalization, after which the signals were summarized for each probe type by taking a median value. The data was found to be of high quality and the Pearson's correlations between the samples were between 0.86 and 0.99 in the different sample groups indicating high reproducibility. The statistical analyses were carried out using Bioconductor's Limma package. For filtering out differentially expressed genes, the minimum fold change limit was set at 2 and false discovery rate (FDR) adjusted significance level at 0.05.
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| |
|
| Submission date |
Aug 01, 2011 |
| Last update date |
Oct 01, 2011 |
| Contact name |
Laura Vesala |
| E-mail(s) |
laura.vesala@jyu.fi
|
| Organization name |
University of Jyväskylä
|
| Department |
Department of Biological and Environmental Science
|
| Street address |
Survontie 9
|
| City |
Jyväskylä |
| ZIP/Postal code |
40100 |
| Country |
Finland |
| |
|
| Platform ID |
GPL14008 |
| Series (1) |
| GSE31103 |
Changes in gene expression during cold exposure in Drosophila montana and D. virilis |
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