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Sample GSM1339191 Query DataSets for GSM1339191
Status Public on Mar 06, 2014
Title 1X4
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 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 35664.24822
42 34464.96613
52 31695.68929
62 31148.74929
63 29628.69026
73 29826.13599
83 28042.01718
93 26688.47538
94 46593.01643
104 46090.99204
114 41528.08078
124 40118.57515
125 15.66816073
135 18.58790084
145 19.74268927
155 16.64197503
156 47101.73872
157 33.73427231
158 0.00573022
159 0.00573022

Total number of rows: 4333

Table truncated, full table size 69 Kbytes.




Supplementary file Size Download File type/resource
GSM1339191_28_UC_102661E_0104_Ranz_1Z4+1X4_350_500_Raw.txt.gz 150.8 Kb (ftp)(http) TXT
Processed data included within Sample table

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