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Sample GSM799053 Query DataSets for GSM799053
Status Public on Jan 06, 2012
Title CCL-125 CHIKV
Sample type SRA
 
Source name larva
Organism Aedes aegypti
Characteristics infection: CCL-125 CHIKV
tissue: larva
days post infection: 4
Extracted molecule total RNA
Extraction protocol 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 (http://www.bioconductor.org). Differential expression analysis between normalized read counts was done using the A-C statistic. We generated Weblogo 3 (http://weblogo.threeplusone.com) plots to analyze the frequency of nucleotide usage in small RNA reads of an identical size class.
 
Submission date Sep 20, 2011
Last update date May 15, 2019
Contact name Kevin Myles
E-mail(s) mylesk@vt.edu
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 GPL14594
Series (1)
GSE32247 Production of Virus-Derived Ping-Pong-Dependent Piwi-like RNAs in the Mosquito Soma
Relations
SRA SRX098238
BioSample SAMN00722943

Supplementary file Size Download File type/resource
GSM799053_CCL125_CHIKR_96hrs_viRNAs.txt.gz 33.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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