|
| Status |
Public on Dec 10, 2019 |
| Title |
shTHOC5 |
| Sample type |
SRA |
| |
|
| Source name |
HepG2
|
| Organism |
Homo sapiens |
| Characteristics |
shRNA: shTHOC5
cell line: HepG2 was derived from a liver hepatocellular carcinoma of a 15 year old Caucasian male.
tissue: liver
disease: Hepatocellular carcinoma
|
| Treatment protocol |
HepG2 cells were infected with lenti virus carry shRNA control and shTHOC5. 3 days after infection, total RNAs were isolated.
|
| Growth protocol |
HepG2 cells were grown in DMEM supplemented with 10% FCS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated using High Pure RNA isolation kit (Roche) in accordance with the manufacturer's recommendations.
RNA-seq libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
bcl2fastq v2.17.1.14 used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Trim Galore!, then mapped to GRCh38 whole genome using bowtie2 (Galaxy Version 2.3.4.1) with parameters -D 20 -R 3 -N 0 -L 20 -i S,1,0.50.
The gene expression values (Fragments Per Kilobase Million (FPKM)) were calculated by Cuffdiff (Galaxy Version 2.2.1.5) using human NONCODEv5 transcript reference.
Genome_build: GRCh38
Supplementary_files_format_and_content: tabular file includes FPKM values for shRNA control sample and shTHOC5 sample
|
| |
|
| Submission date |
May 31, 2018 |
| Last update date |
Dec 10, 2019 |
| Contact name |
Doan Duy Hai Tran |
| E-mail(s) |
[email protected]
|
| Phone |
+495115322857
|
| Organization name |
Hannover Medical School
|
| Department |
Institut of physiological Chemistry
|
| Lab |
AG Tamura-Niemann
|
| Street address |
Carl-Neubergsstr. 1
|
| City |
Hannover |
| State/province |
Niedersachsen |
| ZIP/Postal code |
30625 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE115139 |
Myc/Max dependent long antisense noncoding RNA, EVA1A-AS, participates in survival of hepatocellular carcinoma (HCC) by suppressing anti proliferating gene Eva1A. |
|
| Relations |
| BioSample |
SAMN09288394 |
| SRA |
SRX4145834 |
