|
Status |
Public on Feb 26, 2024 |
Title |
308_D0 |
Sample type |
SRA |
|
|
Source name |
Whole blood
|
Organism |
Homo sapiens |
Characteristics |
tissue: Whole blood subject: 308 infection: DENV-3 study day: 0
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA recovered from Paxgene tubes using the Qiagen PAXgene Blood RNA isolation Kit Libraries created using Illumina Stranded Total RNA Prep with Ribo-Zero Plus Final sequencing libraries generated using the IDT-Ilmn RNA UD Indexes SetA, and QC performed prior to sequencing using the Bioanalyzer and DNA 1000 reagents
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
FASTQs generated using bcl2fastq Kallisto (v0.46.2) was used to pseudoalign samples to the GRCh38 human transcriptome without bootstraps Transcript-level counts and abundance data were imported into R using the TxImport package and TMM normalized using the package EdgeR Assembly: GRCh38 Supplementary files format and content: tab-delimited text file containing raw Kallisto gene count from individual samples
|
|
|
Submission date |
Oct 21, 2022 |
Last update date |
Feb 26, 2024 |
Contact name |
Adam Tully Waickman |
Organization name |
SUNY Upstate Medical University
|
Street address |
766 Irving Avenue
|
City |
Syracuse |
State/province |
New York |
ZIP/Postal code |
13210 |
Country |
USA |
|
|
Platform ID |
GPL24676 |
Series (1) |
GSE216328 |
Transcriptional analysis of DENV-elicited inflammation following experimental human DENV-3 challenge |
|
Relations |
BioSample |
SAMN31407806 |
SRA |
SRX17989421 |