|
| Status |
Public on Nov 19, 2018 |
| Title |
1001701601_I11 |
| Sample type |
SRA |
| |
|
| Source name |
blood (PBMCs)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
patient id: 1-026
cell type: NK cell
Sex: F
diseaseseverity: severe dengue
numberhumanuniquelymappedreads: 1880147
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 |
SAMN09612439 |
| SRA |
SRX4354699 |
