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Sample GSM6480063

Query DataSets for GSM6480063

Status

Public on Dec 19, 2023

Title

DU16-02S0003171_S27

Sample type

SRA

Source name

whole blood

Organism

Homo sapiens

Characteristics

sequencing batch: 2
gender: male
age: 29
site: Sri_Lanka
infection type: Viral
pathogen: Influenza_A_B

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from whole blood collected and stored at -80°C in PAXgene Blood RNA tubes using the PAXgene miRNA Extraction Kit
For batch 1, libraries were constructed using GlobinClear Globin RNA Reduction (Invitrogen) with TruSeq Stranded mRNA Library Kit (Illumina). For batch 2, libraries were contructed using NuGEN Universal Plus mRNA-Seq Library Prep Kit with AnyDeplete Globin depletion (NuGEN/Tecan).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Batch 1 was sequenced on an Illumina HiSeq 2500, and batch 2 was sequenced on an Illumina NovaSeq 6000.
For batch 1, adapters were removed by EA Genomics prior to receipt of sequences. For batch 2, adapters were remvoed using Trimmomatic v0.38.
Reads were aligned to the hg38 reference transcriptome using Bowtie2 with "option --very-sensitive-local"
Express version 1.5.1 was used for quantification at the transcript level. For batch 1 the option "strand rf-stranded" was used, and for batch 2 "strand fr-stranded" was used.
Expression data were normalized using the trimmed mean of M-values approach, specifically using the calcNormFactors function in the edgeR package in R.
Supplementary files format and content: The processed data file contains log2-transformed and normalized counts per million.

Submission date

Aug 18, 2022

Last update date

Dec 19, 2023

Contact name

Emily R. Ko

E-mail(s)

[email protected]

Organization name

Duke University

Department

Medicine