NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8314911 Query DataSets for GSM8314911
Status Public on Nov 21, 2024
Title Coxsackievirus infection at 2 day (replicate 1 of 3)
Sample type SRA
 
Source name derived brain-like endothelial cell
Organism Homo sapiens
Characteristics cell type: derived brain-like endothelial cell
time: 2 days
treatment: virus infected
Treatment protocol iBEC cells were infected with cocksackievirus B3 (in DMSO) for either 2 days or 5 days before RNA was extracted
Growth protocol iBEC cells were grown on Endothelial Cell (EC) media (human endothelial cell serum free medium (Gibco; 11111-044) containing 1% B27 (Gibco; 17504044), 20 ng/mL basic fibroblast growth factor (bFGF) (Peprotech; 100-18B) and 10 µM retinioic acid (RA) (Sigma; 2625)
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted using a NucleoSpin RNA kit (Machery Nagel 740955)
Total RNA was poly-A tail enriched
2 x 150 base paired end libraries; RNA seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Reads were cleaned using TRIMGALORE v 0.4.2 using the default settings
Cleaned reads were mapped to GRCh38.110 genome using STAR version 2.5.3a using the default settings
BAM files were assessed by featureCounts in the Subread package v 2.0.1 using the default settings
Differential expression was analyzed in DeSeq2 v 1.34.0
Supplementary files format and content: comma separated values files contains the raw counts for the 2 day experiments
Supplementary files format and content: comma separated values files contains the raw counts for the 5 day experiments
Assembly: none; clean reads were mapped to annotated human genome (GRch38.110)
 
Submission date Jun 07, 2024
Last update date Nov 21, 2024
Contact name Daryl Lam
E-mail(s) [email protected]
Organization name University of Alabama
Department Biological Sciences
Street address Box 870344
City Tuscaloosa
State/province Alabama
ZIP/Postal code 35487
Country USA
 
Platform ID GPL24676
Series (1)
GSE269413 Transcriptomic analysis of coxsackievirus B3 infection in induced pluripotent stem cell-derived brain-like endothelial cells
Relations
BioSample SAMN41751629
SRA SRX24842174

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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