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| Status |
Public on Feb 24, 2020 |
| Title |
DENV-WT-Aag2 |
| Sample type |
SRA |
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| Source name |
Aedes aegypti Aag-2 cells
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| Organism |
Aedes aegypti |
| Characteristics |
cell line: Aag-2
infection: Dengue virus serotype 2
genotype/variation: DENV-WT
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| Extracted molecule |
total RNA |
| Extraction protocol |
TruSeq Small RNA Library Preparation Kits (Illumina).
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
small RNA
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| Data processing |
Libraries of small RNAs from cell culture were constructed using TruSeq Small RNA Library Preparation Kits (Illumina) according to manufacturer’s instructions. The libraries were sequenced by Illumina HiSeq 2000 at RiboBio. The sequencing reads were mapped to the human genome (release hg19) or mosquito genome (AaeGL5.0) by using Bowite 2.2.5 and the cellular miRNA expression level was determined on the basis of the number of reads that was identical to the annotated miRNA sequences in miRBase version 18, only allowing −2 or +2 nt to be templated by the corresponding genomic sequence at the 3′ end. Viral small RNA (vsRNA) reads which cannot be mapped to human genome were then mapped to DENV2 genome with 100% identity. The subsequent analysis of length and location of these vsRNAs were calculated using in-house Perl scripts. Pairs of complementary 22-nt vsRNAs in each library in different distance categories were computed using principles as previously described (Li et al., 2016; Li et al., 2013).
Genome_build: hg19, AaeGL5.0
Supplementary_files_format_and_content: *_reads.txt: Tab-delimited text files include read sequences and counts.
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| Submission date |
Jun 25, 2019 |
| Last update date |
Feb 24, 2020 |
| Contact name |
xi zhou |
| E-mail(s) |
zhouxi@wh.iov.cn
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| Organization name |
Wuhan University
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| Department |
State Key Laboratory of Virology, College of Life Sciences
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| Street address |
Luojia Hill
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430072 |
| Country |
China |
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| Platform ID |
GPL21020 |
| Series (1) |
| GSE133284 |
Flavivirus induces and antagonizes antiviral RNA interference in both mammals and mosquitoes |
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| Relations |
| BioSample |
SAMN12136611 |
| SRA |
SRX6366219 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3904853_DENV-WT-Aag2_trimmed_unmapped_minusstrand_reads.txt.gz |
68.2 Kb |
(ftp)(http) |
TXT |
| GSM3904853_DENV-WT-Aag2_trimmed_unmapped_plusstrand_reads.txt.gz |
62.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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