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Sample GSM2043765 Query DataSets for GSM2043765
Status Public on Feb 02, 2016
Title 240614 0518-370neg ILC3
Sample type SRA
 
Source name Peripheral Blood
Organism Homo sapiens
Characteristics individual: 0518-370neg
cell type: Innate Lymphoid Cell 3
hiv status: HIV-
days post hiv-infection: uninfected
Treatment protocol Cells were sorted into RLT buffer by FACS, spun down, and snap frozen on dry ice.
Extracted molecule total RNA
Extraction protocol Due to low cell counts, lysates were treated as single cells in an adapted SMART-Seq II protocol (Trombetta et al., Current Protocols in Molecular Biology, 2014, 107:II:4:22). Briefly, mRNA was extracted from lystates using SPRI beads and then reverse transcribed and amplified using a poly-adenylated RT primer and template switching SMART oligo.
Library construction followed from the protocol above (Trombetta et al.,).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description ILC_matrix_processed.txt
Data processing Illumina bcl2fastq2.15.0.4 was used to generate .fastq files from .bcl files.
tophat2 was used to align the scRNA-seq data
rsem-1.2.3 generated an expression matrix in psuedocounts
Genome_build: hg19 ucsc genomestudio
edgeR modeled dispersion, normalized for library size, and conducted differential expression likelihood ratio tests
Supplementary_files_format_and_content: edgeR normalized counts per million with genes as rows and cell populations (samples) as columns
 
Submission date Jan 21, 2016
Last update date May 15, 2019
Contact name Alasdair Leslie
E-mail(s) al.leslie@ahri.org
Organization name African Health Research Institute
Lab Leslie Lab
Street address 719 Umbilo Road
City Durban
ZIP/Postal code 4001
Country South Africa
 
Platform ID GPL18573
Series (1)
GSE77088 Time course RNA-Seq of Innate Lymphoid Cells in Early Acute HIV Infection
Relations
BioSample SAMN04432874
SRA SRX1539856

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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