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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 30, 2017 |
| Title |
DENV_D6 |
| Sample type |
SRA |
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| Source name |
Whole mosquito
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| Organism |
Aedes aegypti |
| Characteristics |
strain: Liverpool strain
tissue: Whole mosquito
age: 7days
treatment: microinjected with 100 M.I.D.50 viruses
extracted timepoint: 6 day
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| Treatment protocol |
7 days old mosquitos were microinjected with 100 M.I.D. 50 virus, then infected after 1, 6 days.
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| Growth protocol |
Aedes Aegypti was reared at 28℃ and 80% humidity.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Whole mosquito were dissected from mosquitoes, and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
microinjected with 100 M.I.D.50 viruses
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| Data processing |
HCS 2.012 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Aedes Aegypti genome using SOAPaligner/SOAP2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Annotating to the KEGG database by BLAST(-p blastx -e 1e-5 -m 8).
Annotating the results that from BLAST(-p blastx -e 1e-5 -m 7)sequences to Nr database of NCBI to the terms of GO by use BLAST2GO(default parameters).
NOIseq method coming from Sonia Tarazona et al., Genome Research, 2011., was applied to screen differentially expressed genes between two groups
Genome_build: Aaegl3.3
Supplementary_files_format_and_content: Excel files include RPKM values, log2 ratio, P values, FDR, KEGG Orthology, and GO analysis for each Sample ...
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| Submission date |
Dec 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yibin Zhu |
| E-mail(s) |
zhuyibin@mail.tsinghua.edu.cn
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| Phone |
8618515653980
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| Organization name |
Tsinghua University
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| Department |
School of Medicine
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| Street address |
Biotechnology building
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| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL21020 |
| Series (2) |
| GSE91027 |
Mosquito hematophage-mediated GABAergic activation facilitates acquisition of mosquito-borne viruses (infection) |
| GSE91034 |
Mosquito hematophage-mediated GABAergic activation facilitates acquisition of mosquito-borne viruses |
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| Relations |
| BioSample |
SAMN06121356 |
| SRA |
SRX2404709 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2419907_Mock_D6-VS-DENV2_D6.GeneDiffExp.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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