|
Status |
Public on Nov 19, 2018 |
Title |
1001701601_N17 |
Sample type |
SRA |
|
|
Source name |
blood (PBMCs)
|
Organism |
Homo sapiens |
Characteristics |
tissue: blood patient id: 1-026 cell type: T cell Sex: F diseaseseverity: severe dengue numberhumanuniquelymappedreads: 1421732 numbervirusreads: 0 age: 25
|
Extracted molecule |
total RNA |
Extraction protocol |
No extraction, single cells are sorted into 0.4ul lysis buffer Cells are lysed in lysis buffer containing Triton X-100, then RT using template switching oligo and preamplification for 21 cycles as in SmartSeq2 is performed. Cells with different levels of intracellular virus are cherry picked and sequencing libraries are made using illumina’s Nextera XT kit.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
bcl2fastq demux STAR mapping Htseq-count 0.7+ gene counting Stampy virus mapping Custom script for filtering virus reads Genome_build: grch38 Supplementary_files_format_and_content: One TSV for each sample containing the counts of gene expression.
|
|
|
Submission date |
Jul 05, 2018 |
Last update date |
Nov 19, 2018 |
Contact name |
Fabio Zanini |
E-mail(s) |
fabio.zanini@fastmail.fm
|
Organization name |
University of New South Wales
|
Lab |
Zanini
|
Street address |
High and Botany St
|
City |
Kensington |
State/province |
NSW |
ZIP/Postal code |
2033 |
Country |
Australia |
|
|
Platform ID |
GPL24676 |
Series (1) |
GSE116672 |
In vivo molecular signatures of severe dengue infection revealed by viscRNA-Seq |
|
Relations |
BioSample |
SAMN09612400 |
SRA |
SRX4354820 |