NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2230826 Query DataSets for GSM2230826
Status Public on Aug 09, 2016
Title Dengue virus 36 hs replicate B
Sample type SRA
 
Source name A549_Dengue virus 36 hs
Organism Homo sapiens
Characteristics cell line: A549
infected with: Dengue virus 2
time point: 36 hours post infection
Treatment protocol The cells where infected with Dengue virus 2 or Mock 1 h at 37°C (MOI 10)
Growth protocol Standard conditions for A549 infected cells
Extracted molecule total RNA
Extraction protocol mRNA was purified using Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description processed data column: DV36B
Data processing Base
Sequence reads were mapped to Homo sapiens UCSC hg19 genome using TopHat v2.1.1 with default parameters
Count tables for different feature levels were obtained from bam files using custom R v3.0.2 scripts.
Differential gene expression was estimated using edgeR package version 3.4.2 and resulting p-values were adjusted using false discovery rate (fdr) criterion.
The transcriptome was partitioned into subgenic joint features called bins and labeled as exon-bin, intron-bin or alternative-splicing (AS) bins. In addition AS-bins were further classified as exon skipping (ES), 5’ or 3’ alternative (5´alt, 3´alt), intron retention (IR) or multiple. Bins from monoexonic genes, with mean count values lower than 5 reads per condition and rd bin / rd gen lower than 0.05 were discarded.
COPIAR DE MyM
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Comprehensive spreadsheets with the results of the analysis of differential splicing detailed above
 
Submission date Jul 12, 2016
Last update date May 15, 2019
Contact name Andrea Gamarnik
E-mail(s) agamarnik@leloir.org.ar
Organization name Fundacion Instituto Leloir
Street address Av. Patricias Argentinas 435
City Ciudad Autonoma de Buenos Aires
ZIP/Postal code C1405BWE
Country Argentina
 
Platform ID GPL20301
Series (1)
GSE84285 Genome-wide analysis of Dengue virus 2 infected cells
Relations
BioSample SAMN05375345
SRA SRX1934567

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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