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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
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|
|
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)
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|
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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 |