NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1468369 Query DataSets for GSM1468369
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

Supplementary file Size Download File type/resource
GSM1468369_WNV_2_fpkm.txt.gz 161.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap