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Sample GSM1219433 Query DataSets for GSM1219433
Status Public on Dec 31, 2014
Title Larvae
Sample type SRA
 
Source name The whole body
Organism Bactrocera dorsalis
Characteristics developmental stage: larva
Extracted molecule total RNA
Extraction protocol About 2000 eggs, 10 larvae, 10 pupae and 8 adults were gathered into four centrifuge tubes, respectively, and stored at −80 °C for RNA extraction. Total RNA from the four samples was extracted using the TriZol reagent (TransGen Biotech, Beijing, China), according to the manufacturer's instructions.
For each library, small RNAs of 18 to 30 bp in length were separated by 15% polyacrylamide gel electrophoresis (PAGE). The ligation between these small RNAs and a 5' and 3' adaptors was performed using T4 RNA Ligase (Takara:D2050). The 5'- and 3'-ligated RNA products were purified and then reverse transcribed for the first-strand cDNA using a SuperScript® II Reverse Transcriptase kit (InvitrogenTM: 18064-014) with the complementary sequence of the 3' adaptor. Thereafter, the cDNAs were used as templates for double-stranded cDNA synthesis using PCR amplification in a Veriti Thermal Cycler (Applied Biosystems), using primers that anneal to the adapters. After second-strand cDNA synthesis, the adaptor sequence primers were used to amplify the PCR products as a small RNA library for deep sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer
 
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to the transcriptome of Bactrocera dorsalis using SOAP software.
Normalize the expression of miRNA in two samples (control and treatment) to get the expression of transcript per million (TPM). Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads*1000000
 
Submission date Aug 29, 2013
Last update date May 15, 2019
Contact name Yong Huang
E-mail(s) zhugezhengwu@163.com
Organization name Southwest University
Street address Tiansheng Road
City Chongqing
ZIP/Postal code 400716
Country China
 
Platform ID GPL17657
Series (1)
GSE50450 Deep sequencing of small RNA libraries reveals dynamic expression patterns of miRNAs in multiple developmental stages of Bactrocera dorsalis
Relations
BioSample SAMN02339384
SRA SRX341407

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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