|
| Status |
Public on Jan 02, 2019 |
| Title |
Huh7 AdPCK1 rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Huh 7 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hepatoma cells
tissue: liver
adenovirus: adenovirus overexpression PCK1
|
| Treatment protocol |
Adenoviral recombinant AdGSTZ1 or AdPCK1 were generated using the AdEasy system, and green fluorescent protein-expressing analogous adenovirus (AdGFP) was used as a control.
|
| Growth protocol |
Huh7 cells were cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum, 100 IU penicillin, and 100 mg/ml streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells using TRIzol reagent (Invitrogen)
cDNA Library Construction: The cDNA libraries were constructed for each pooled RNA sample using the VAHTSTM Total RNA-seq (H/M/R) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: depletion of rRNA and fragmented into 150-200 bp using divalent cations at 94 ℃ for 8 min. The cleaved RNA fragments were reverse-transcribed into first-strand cDNA, second-strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. Target bands were harvested through VAHTSTM DNA Clean Beads .The products were purified and enriched by PCR to create the final cDNA libraries and quantified by Agilent2200. The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina Xten with 51 plus 7 cycles by NovelBio Corp. Laboratory, Shanghai.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
All_Counts.txt
|
| Data processing |
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
MapSplice mapping to reference genome
count counting
Genome_build: GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample
|
| |
|
| Submission date |
Jul 27, 2018 |
| Last update date |
Jan 02, 2019 |
| Contact name |
tang ni |
| E-mail(s) |
[email protected]
|
| Organization name |
Chongqing Medical University
|
| Street address |
yixueyuan Road NO.1
|
| City |
chongqing |
| ZIP/Postal code |
400016 |
| Country |
China |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE117822 |
Transcriptome Analysis of Huh7 cells Infected with Adenovirus Overexpression GSTZ1 or PCK1 |
|
| Relations |
| BioSample |
SAMN09729016 |
| SRA |
SRX4478271 |
