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Sample GSM1339192 Query DataSets for GSM1339192
Status Public on Mar 06, 2014
Title 1Y2
Sample type RNA
 
Source name whole flys
Organism Drosophila melanogaster
Characteristics genotype: Oregon-R
gender: Male
development state: PF
Treatment protocol Samples were snap frozen in liquid nitrogen and stored at -80⁰C until RNA isolation.
Growth protocol Flies were grown in standard corn meal medium, constant lighting conditions, and at 25⁰C, larvae were raised under non-crowded conditions in medium with 0.05% bromophenol blue.
Extracted molecule total RNA
Extraction protocol ~120 mg (60-80 individuals depending on the strain) of frozen flies for each biological replicate were grinded using motorized pestles and the total RNAs extracted and purified with miRVana miRNA isolation kit (Ambion Inc.). Both total RNAs and small RNAs from biological replicates for each strain/sex were isolated and used in all three expression profiling approaches. Concentration, quality and integrity of the RNA samples were assessed using the NanoDrop 8000 Spectrophotometer and the RNA 6000 Nano and Small RNA kits (Agilent Technologies) in an Agilent 2100 Bioanalyzer. RNA extractions for different strains were performed independently to avoid cross-contamination.
Label Cy5
Label protocol Performed by LC Sciences
 
Hybridization protocol Performed by LC Sciences
Scan protocol Performed by LC Sciences
Data processing For a given array, the Cy3 and Cy5 fluorescent intensity values of each array were first adjusted by subtracting local background and then normalized according to a locally-weighted regression approach. The adjusted values were further log2-transformed and normalized across arrays using the quantile method implemented in JMP Genomics 5.0. The expression values for the 280 reporters relevant to the six strains of interest were obtained by averaging over the three technical replicates spotted on separate blocks of the array. A linear model was used to test for differences in expression levels between developmental stages in any given strain by sex combination and for differences in expression levels between the sexes in any given strain by developmental stage combination.
 
Submission date Mar 04, 2014
Last update date Mar 06, 2014
Contact name Xiao-Qin Xia
E-mail(s) xqxia@ihb.ac.cn
Organization name Institute of Hydrobiology, the Chinese Academy of Sciences
Department Center for Molelcular and Cellular Biology of Aquatic Organisms
Lab Aquatic Bioinformatics
Street address No. 7 Donghu South Road, Wuchang District
City Wuhan
State/province Hubei
ZIP/Postal code 430072
Country China
 
Platform ID GPL18365
Series (1)
GSE55562 Evolution of microrna expression at the onset of drosophila metamorphosis by miRNA

Data table header descriptions
ID_REF
VALUE Intensity values without log2-transformation are present for expression level.

Data table
ID_REF VALUE
32 34482.62462
42 36106.90059
52 36309.07317
62 34406.33332
63 24804.95587
73 25211.59753
83 25912.28121
93 25031.82213
94 12792.6696
104 15798.03874
114 16375.37743
124 15831.45203
125 17.6627152
135 16.20131908
145 17.84652106
155 14.76882256
156 36238.49691
157 24.30683659
158 0.070603873
159 6.997282135

Total number of rows: 4333

Table truncated, full table size 70 Kbytes.




Supplementary file Size Download File type/resource
GSM1339192_01_G4.2_UC_101296B_0629_Ranz_1W2+1Y2_420_500_Raw.txt.gz 154.3 Kb (ftp)(http) TXT
Processed data included within Sample table

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