GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM829391 Query DataSets for GSM829391
Status Public on Jan 06, 2012
Title C6/36 CHIKV B2(FHV) rep3 (truSeq)
Sample type SRA
Source name larva
Organism Aedes albopictus
Characteristics infection: C6/36 CHIKV B2(FHV)
days post infection: 4
tissue: larva
Extracted molecule total RNA
Extraction protocol total and viral RNA, As described in Illumina's Small RNA sample preparation guide (Cat# FC-102-1009)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
Data processing After removal of adaptor sequences and non-coding RNA sequences (rRNAs, tRNAs, snoRNAs, etc.) processed reads were mapped to the CHIKV genome (strain 37997) using Bowtie (v-mode, permitting 1 mismatch). In order to compare small RNA reads between libraries we normalized using the TMM method implemented by the edgeR software package ( Differential expression analysis between normalized read counts was done using the A-C statistic. We generated Weblogo 3 ( plots to analyze the frequency of nucleotide usage in small RNA reads of an identical size class.
Submission date Nov 07, 2011
Last update date May 15, 2019
Contact name Kevin Myles
Phone (540) 231-6158
Organization name Virginia Tech
Department Fralin Life Science Institute
Lab Myles
Street address Fralin Biotechnology Center
City Blacksburg
State/province VA
ZIP/Postal code 24061
Country USA
Platform ID GPL14595
Series (1)
GSE32247 Production of Virus-Derived Ping-Pong-Dependent Piwi-like RNAs in the Mosquito Soma
SRA SRX104939
BioSample SAMN00750643

Supplementary file Size Download File type/resource
GSM829391_C636_CHIK_FHVB2_rep3_viRNAs.txt.gz 2.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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