|
| Status |
Public on Dec 26, 2018 |
| Title |
TXNDC9-KO rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HepG2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
genotype/variation: TXNDC9 knockout
|
| Treatment protocol |
The CRISPR-Cas9 system were used for TXNDC9 knockout.
|
| Growth protocol |
HepG2 cells were cultured in DMEM supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from wild-type or TXNDC9 knockout HepG2 cells using TRIzol Reagent (ThermoFisher Scientific, USA) according to manufacturer’s protocol. Sequencing were performed at the illumina Hiseq Xten platform.
Polyadenylated RNA was isolated from 5 g total RNA with the mRNA Capture Beads. RNA-seq library were constructed with VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Vazyme Biotech Co, Nanjing, China) according to manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
all_FPKM_expression.txt
|
| Data processing |
Reads were mapping to human genome (hg38) using TopHat2 with a reference annotation from ensemble database. no-novel-juncs options were used to ignore de novo gene and transcript identification.
Gene expression profile of each samples as well as differentially expressed genes between wild-type and TXNDC9 knockout HepG2 cells were identified using the cuffdiff suite from cufflinks.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
|
| |
|
| Submission date |
Apr 19, 2018 |
| Last update date |
Dec 26, 2018 |
| Contact name |
Dawei Chen |
| E-mail(s) |
dwchen85@163.com
|
| Organization name |
School of Medicine, Southeast University
|
| Department |
Jiangyin People's Hospital
|
| Street address |
No. 163, Shoushan Road
|
| City |
Jiangyin |
| State/province |
Jiangsu |
| ZIP/Postal code |
214400 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE113400 |
Determine the role of TXNDC9 in hepatocellular carcinoma progression |
|
| Relations |
| BioSample |
SAMN08956923 |
| SRA |
SRX3973934 |
