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Sample GSM1701372 Query DataSets for GSM1701372
Status Public on Jun 03, 2015
Title 50d_autumn_D_a
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.
 
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

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
1 273.2324859
2 655.2945179
3 147.3017754
4 17.16269502
5 958.8644168
6 15.29230032
7 381.5163326
8 6.722347571
9 9.159142717
10 5.242066478
11 6.786157723
12 15.79365113
13 1731.637222
14 142.5754193
15 907.1111386
16 22.72828716
17 43.8403281
18 15.18008675
19 3.175999957
20 5.450902495

Total number of rows: 1850

Table truncated, full table size 29 Kbytes.




Supplementary file Size Download File type/resource
GSM1701372_US83400189_252669110004_S01_GE1_107_Sep09_1_4.txt.gz 758.4 Kb (ftp)(http) TXT
Processed data included within Sample table

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