|
| Status |
Public on Mar 06, 2014 |
| Title |
1X1 |
| Sample type |
RNA |
| |
|
| Source name |
whole flys
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: Oregon-R
gender: Female
development state: >=18BPF
|
| 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 |
Cy3
|
| 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 |
|
