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Sample GSM2253837 Query DataSets for GSM2253837
Status Public on Jul 01, 2021
Title Jc1-E2FLAGv_9
Sample type SRA
 
Source name Huh7.5.1 cell_HCV-infected
Organisms Homo sapiens; Hepacivirus hominis
Characteristics cell line: Huh7.5.1
cell type: DMSO-differentiated Huh7.5.1 cell
treatment: Jc1E2FLAG HCV
Treatment protocol DMSO-differentiated Huh7.5.1 cells were infected or not using HCV cell-culture derived particles (HCVcc Jc1E2FLAG). On day 7 post-infection, single-cells were sorted into 96-well plates using a well-established limiting dilution assay. Single-cells were lysed in 5 µl TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol. Cellular mRNA was isolated using the RNeasy mini kit (Qiagen) and sequenced using the SMART-Seq 2 procedure described by Trombetta et a, 2014 on one NextSeq500. HCV RNA was co-amplified with cellular mRNA using a SMART-compatible primer (sequence: 5'-Biotin-AAGCAGTGGTATCAACGCAGAGTACTCTGCGGAACCGGTGAGTA-3')). The modulation of specific gene signatures in association with the normalized HCV copy number in single cell RNA-Seq data was determined using the pre-ranked GSEA module implemented in GenePattern with Pearson correlation as the rank metric.
Growth protocol For proliferation arrest and differentiation, Huh7.5.1 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) containing 1% DMSO for 10 days, followed by additional 7 days after HCV infection.
Extracted molecule total RNA
Extraction protocol RNA was isolated using the RNeasy kit (Qiagen) according to manufacturer 's protocol.
Refer to Trombetta et al, 2014
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Single-cell RNA-Seq
HCV-infected
Data processing Reads were aligned to the human (hg19 UCSC) and HCV (Jc1) reference genomes using TopHat with default setttings.
Human gene expression levels were quantified using Cuffquant (Cufflinks 2.2.1 suite) with default settings.
Human gene expression levels were normalized across all samples using Cuffnorm (Cufflinks2.2.1 suite) with default settings.
HCV copy number was calculated as the percentage of viral read pairs mapped relative to all human and viral read pairs mapped.
Genome_build: hg19 UCSC and HCV Jc1
Supplementary_files_format_and_content: [.txt] Tab-delimited text files with human gene expression levels (FPKM) and HCV copy number for each sample.
 
Submission date Jul 27, 2016
Last update date Jul 01, 2021
Contact name Thomas F Baumert
Organization name Inserm U1110
Department University of Strasbourg
Street address 3, rue Koeberlé
City Strasbourg
ZIP/Postal code 67000
Country France
 
Platform ID GPL21805
Series (2)
GSE66843 A cell-based model unravels drivers for hepatocarcinogenesis and targets for clinical chemoprevention
GSE81040 High-throughput single-cell RNA-Seq profiling of DMSO-differentiated Huh7.5.1 undergoing or not long-term HCV infection
Relations
BioSample SAMN05449238
SRA SRX1980095

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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