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| Status |
Public on Dec 31, 2014 |
| Title |
Eggs |
| Sample type |
SRA |
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| Source name |
The whole body
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| Organism |
Bactrocera dorsalis |
| Characteristics |
developmental stage: egg
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
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| 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
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| Submission date |
Aug 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yong Huang |
| E-mail(s) |
zhugezhengwu@163.com
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| Organization name |
Southwest University
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| Street address |
Tiansheng Road
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| City |
Chongqing |
| ZIP/Postal code |
400716 |
| Country |
China |
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| 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 |
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| Relations |
| BioSample |
SAMN02339382 |
| SRA |
SRX341406 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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