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Sample GSM6668885 Query DataSets for GSM6668885
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

Supplementary file Size Download File type/resource
GSM6668885_21105FL-02-20.abundance.tsv.gz 2.6 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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