|
| Status |
Public on Jan 12, 2023 |
| Title |
HepG2_siFASRL_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HCC cell lines
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HCC cell lines
tissue: liver
cell line: HepG2
treatment: siFASRL
|
| Treatment protocol |
HCC cells with the treatment of siFASRL or siNC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from HCC cells were extracted using Trizol method.
Total RNA was extracted from the cells using Trizol (Invitrogen, USA), qualified and quantified using a Nano Drop and Agilent 2100 Bioanalyzer (Thermo Fisher Scientific, USA). Afterwards, oligo(dT)-attached magnetic beads were purified mRNA. First-strand cDNA and second-strand cDNA were respectively synthesized. The single strand circle DNA was formatted as the final library, and then was subjected to sequencing on BGIseq500 platform. The library preparation and sequencing were conducted by BGI Genomics (Shenzhen, China).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
The RNA-seq data was filtered with SOAPnuke, and clean reads were obtained.
The clean data were mapped to reference genome using HISAT2, and were aligned to reference coding gene set by Bowtie2.
Then, expression of genes was calculated using by RESM.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Jun 21, 2022 |
| Last update date |
Jan 12, 2023 |
| Contact name |
Li Peng |
| E-mail(s) |
pengli9@mail.sysu.edu.cn
|
| Phone |
+86 20 81332402
|
| Organization name |
Sun Yat-Sen Memorial Hospital
|
| Street address |
No. 107 Yanjiang West Road
|
| City |
Guangzhou |
| ZIP/Postal code |
510120 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (2) |
| GSE206548 |
Superenhancer-driven lncRNA FASRL in hepatocellular carcinoma [RNA-seq] |
| GSE206549 |
Superenhancer-driven lncRNA FASRL in hepatocellular carcinoma |
|
| Relations |
| BioSample |
SAMN29221874 |
| SRA |
SRX15806784 |
