|
| Status |
Public on Jun 03, 2015 |
| Title |
50d_autumn_D_c |
| Sample type |
RNA |
| |
|
| Source name |
whole tissue, 50-day-old diapausing female
|
| Organism |
Drosophila montana |
| Characteristics |
strain: 175OJ8
state: diapausing
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared with Ambion RNAqueous 96 well total RNA Isolation Kit with DNase treatment (Qiagen) and purified with MinElute kit (Qiagen). 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 |
Jun 02, 2015 |
| Last update date |
Jun 03, 2015 |
| Contact name |
Tiina Susanna Salminen |
| E-mail(s) |
tiina.s.salminen@uta.fi
|
| Phone |
044-5935734
|
| Organization name |
University of Tampere
|
| Department |
BioMediTech
|
| Street address |
Biokatu 6, Finn-Medi 1
|
| City |
Tampere |
| ZIP/Postal code |
33520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL14008 |
| Series (1) |
| GSE69202 |
Seasonal gene expression kinetics between diapause phases in Drosophila virilis group speciesand overwintering differences between diapausing and non-diapausing females |
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