|
| Status |
Public on May 07, 2014 |
| Title |
A3 |
| Sample type |
SRA |
| |
|
| Source name |
Culex pipiens quinquefasciatus
|
| Organism |
Culex quinquefasciatus |
| Characteristics |
tissue: lavae
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of 30 mosquito larvae of each was extracted using the TRIzol. Total RNA samples were pooled and 10 mg from each pool was used to isolate poly(A) mRNA and to prepare non-directional Illumina RNA-Seq libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The Cx. pipiens quinquefasciatus genome and gene information were downloaded from the quinquefasciatus Genome Annotation Project (https://www.vectorbase.org/organisms/culex-quinquefasciatus, GenBank accession number: AAWU00000000.1).
The remaining reads were aligned to the mosquito genome using SOAPaligner/soap2.
ERANGE software (version 4.0) (http://woldlab.caltech.edu/gitweb/) was used to calculate normalized gene locus expression levels by assigning reads to their site of origin and counting them. The expression level of a gene from RNA-Seq was normalized by the RPKM (reads per kilo bases per million reads) value.
The R package DEGseq was applied to identify DEGs with a random sampling model based on the read count for each gene in each mosquito population.
Genome_build: Mosquito Genome Annotation Project (Vectorbase) https://www.vectorbase.org/organisms/culex-quinquefasciatus
Supplementary_files_format_and_content: text files include RPKM values for each Sample
|
| |
|
| Submission date |
May 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Chunxiao Li |
| E-mail(s) |
[email protected]
|
| Phone |
+8613681559005
|
| Organization name |
Beijing Institute of Microbiology and Epidemiology
|
| Street address |
20 Dongdajie, Fengtai District
|
| City |
Beijing |
| ZIP/Postal code |
100071 |
| Country |
China |
| |
|
| Platform ID |
GPL14891 |
| Series (1) |
| GSE57307 |
Culex pipiens pallens and Cx. p. quinquefasciatus with different resistant level |
|
| Relations |
| BioSample |
SAMN02746140 |
| SRA |
SRX533494 |
