|
Status |
Public on Oct 01, 2015 |
Title |
WNV rep2 |
Sample type |
SRA |
|
|
Source name |
Cell line
|
Organism |
Culex quinquefasciatus |
Characteristics |
treatment: infected with West Nile Virus
|
Treatment protocol |
Cells were infected with West Nile virus (NY99-4132 strain) for 48 hours
|
Growth protocol |
Hsu cells were maintained in L15 media at 28C
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using Qiagen RNeasy kit; mRNA was prepared using polydT columns 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 |
Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Culex quinquefasciatus transcriptome (CpipJ2) tophat 1.4 with parameters --read-mismatches 5 --splice-mismatches 2 --min-anchor-length 5 --min-intron-length 30 --no-novel-juncs --library-type fr-unstranded Data analysis followed using protocol given in Trapnell et al 2012 Genome_build: CpipJ2 Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
|
|
Submission date |
Aug 08, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Prasad N Paradkar |
Organization name |
CSIRO-AAHL
|
Street address |
5 Portarlington Road
|
City |
Geelong |
State/province |
Victoria |
ZIP/Postal code |
3220 |
Country |
Australia |
|
|
Platform ID |
GPL14891 |
Series (1) |
GSE60229 |
Transcriptome analysis of Culex cells after West Nile virus infection |
|
Relations |
BioSample |
SAMN02978996 |
SRA |
SRX672339 |