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| Status |
Public on May 23, 2016 |
| Title |
NS1-18h |
| Sample type |
SRA |
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| Source name |
Midguts
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| Organism |
Aedes aegypti |
| Characteristics |
strain: Liverpool
gender: female
age: 7days
protocol: blood fed DENV2 NS1
time: 18h
tissue: Midguts
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| Treatment protocol |
7 days old mosquitos were blood fed BSA or DENV2 NS1, then treated after 4, 8,18 hours.
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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 |
Midguts 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 |
18h BSA-VS-NS1.GeneDiffExp.txt
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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: .txt files include RPKM values, log2 ratio, P values, FDR, KEGG Orthology, and GO analysis for each Sample ...
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| Submission date |
Oct 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
jianying Liu |
| E-mail(s) |
316721214@qq.com
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| Phone |
18811361620
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| Organization name |
tsinghua university
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| Street address |
Room 4-305,Biotechnology building, Tsinghua University, Beij
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| City |
beijing |
| State/province |
beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL21020 |
| Series (1) |
| GSE73967 |
The midguts transcriptome of Aedes aegypti (Liverpool strain) females blood fed DENV2 NS1 versus those blood fed BSA |
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| Relations |
| BioSample |
SAMN04161020 |
| SRA |
SRX1331704 |
| 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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