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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 18, 2020 |
| Title |
None infected Huh7.5.1 cells |
| Sample type |
SRA |
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| Source name |
Huh7.5.1 cell line
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Hepatoma cell
passage: Passage 4
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| 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.
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| 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.
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| 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
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Ion Torrent Proton |
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| 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
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| Submission date |
Aug 13, 2020 |
| Last update date |
Aug 18, 2020 |
| Contact name |
Chen Xu |
| E-mail(s) |
chenxu8836@hotmail.com
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| Phone |
+86-13774294166
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| Organization name |
The Second Military Medical University
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| Street address |
No, 800, Rd. Xiangyin
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| City |
Shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
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| Platform ID |
GPL17303 |
| Series (1) |
| GSE156205 |
Small RNA sequencing of HCV infected hepatoma cells |
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| Relations |
| BioSample |
SAMN15813957 |
| SRA |
SRX8944514 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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