|
| 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 |
