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Sample GSM3249584 Query DataSets for GSM3249584
Status Public on Nov 19, 2018
Title 1001701601_C11
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: 1958603
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 SAMN09612213
SRA SRX4354561

Supplementary file Size Download File type/resource
GSM3249584_1001701601_C11_counts.tsv.gz 166.4 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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