|
| Status |
Public on Jan 04, 2017 |
| Title |
HepG2 cells expressing ATP7B WT, biological rep3 |
| Sample type |
SRA |
| |
|
| Source name |
HepG2 cells expressing ATP7B WT
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2 hepatocellular carcinoma cell line
gender: male
genotype/variation: overexpressing ATP7B WT
|
| Treatment protocol |
The cells, after 24 hour of plating, were infected with adenovirus. The cells infected were grown for 48 hours. Cells were treated with 1uM JNKinhibitor (SP600125, Sigma Aldrich) or 5uM p38inhibitor (SB202190, Sigma Aldrich) for 24 hours. After the treatment, the cells were scraped with a lysis buffer (Qiagen)
|
| Growth protocol |
The cells were grown for 72 hours at 37°C in 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).
Total RNA (500 ng) from each sample was prepared using TruSeq RNA sample prep reagents (Illumina, San Diego, CA, USA) according to manufacturer's instructions
The amplified fragmented cDNA of ∼200 bp in size were sequenced in paired-end mode using the HiSeq 2000 (Illumina) with a read length of 2×100 bp
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
Adeno ATP7BWT3
Gene expression data from cells infected with adenovirus expressing ATP7B wt -GFP
cell line derived from the liver tissue of a Caucasian American male
|
| Data processing |
Reads were aligned and assigned to Human Gencode release 19 transcripts and genes by using RSEM version 1.2.19 with standard parameters (Li & Dewey, 2011).
Genome_build: Human Gencode release 19
Supplementary_files_format_and_content: tab-delimited text files include raw counts and FPKM values for each Sample
|
| |
|
| Submission date |
Apr 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Annamaria Carissimo |
| E-mail(s) |
carissimo@tigem.it
|
| Organization name |
Tigem
|
| Street address |
via Castellino
|
| City |
Napoli |
| ZIP/Postal code |
80131 |
| Country |
Italy |
| |
|
| Platform ID |
GPL15433 |
| Series (1) |
| GSE80361 |
Transcriptome profile of HepG2-expressing ATP7B-H1069Q (liver hepatocellular cells) exposed to JNK or p38 Inhibitor |
|
| Relations |
| BioSample |
SAMN04866870 |
| SRA |
SRX1710753 |
