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Sample GSM4726725 Query DataSets for GSM4726725
Status Public on Aug 18, 2020
Title 48 hours after HCV infection in Huh7 cells
Sample type SRA
 
Source name Huh7 cell line
Organism Homo sapiens
Characteristics tissue: Hepatoma cell
passage: Passage 4
Treatment protocol The Japanese fulminant hepatitis type 1 (JFH-1) plasmid was linearized and transcribed in vitro to produce HCV RNA using a MEGAscript kit (Promega, Madison, WI, USA). Then, 106 hepatoma cells were transfected with 10 ng of viral RNA by electroporation. The cells were moved to culture plates for further viral amplification, and the medium was changed for fresh medium 4 h later. The supernatant was collected 96 h after transfection and filtered through a 0.45-μm membrane. HCVcc was then concentrated and purified by ultracentrifugation, and viral titers were determined for later experiments.
Growth protocol Human hepatoma Huh7 and Huh7.5.1 cells were cultured in Dulbecco’s modified Eagle medium (DMEM, Life Technologies, USA) supplemented with 10% fetal bovine serum (FBS), 1× nonessential amino acids, 100 IU/ml streptomycin and penicillin, and 2 mM L-glutamine (Gibco, Invitrogen). Cells were incubated under an atmosphere with 5% CO2 at 37℃ for subsequent use in experimental procedures.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
smallRNA libraries were prepared for sequencing using standard Ion Proton Protocols
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Ion Torrent Proton
 
Data processing Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Utilizing the BWA software, we mapped the clean data to miRBase 21.0 human miRNA database and human genome.
count counting
Genome_build: GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample
 
Submission date Aug 13, 2020
Last update date Aug 18, 2020
Contact name Chen Xu
E-mail(s) chenxu8836@hotmail.com
Phone +86-13774294166
Organization name The Second Military Medical University
Street address No, 800, Rd. Xiangyin
City Shanghai
ZIP/Postal code 200433
Country China
 
Platform ID GPL17303
Series (1)
GSE156205 Small RNA sequencing of HCV infected hepatoma cells
Relations
BioSample SAMN15813958
SRA SRX8944513

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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