|
| Status |
Public on Apr 16, 2020 |
| Title |
S943Nr15 |
| Sample type |
SRA |
| |
|
| Source name |
HepaRG cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Methyleugenol
cas number: 93-15-2
concentration: 250 uM
|
| Treatment protocol |
Differentiated HepaRG cells were treated with the non toxic concentrations of 1 µM aflatoxin B1, 5 µM benzo[a]pyrene, 1 µM lasiocarpine, 250 µM methyleugenol or 20 mM nitrosopyrrolidine for 24h.
|
| Growth protocol |
HepaRG cells were seeded in 6-well-plates (200 00 cells per well) and cultivated and proliferated in Williams E medium with 2 mM glutamine supplemented with 10 % fetal calf serum, 100 U/mL penicillin, 100 µg/mL streptomycin, 0.05 % human insulin and 50 µM hydrocortison. After a 2-week proliferation phase, cells were differentiated in the mentioned culture medium additionally containing 1.7 % DMSO, for another 2 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was performed with the RNeasy Mini Kit (Qiagen) according to the manufactures' protocol.
Libraries were prepared from 100 ng of RNA using the TruSeq Stranded Total RNA kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
De-multipltiplexing of sequencing reads was accomplished using Illumina bcl2fastq (version 2.19)
Adapter trimming was performed with Skewer (version 0.2.2)
Alignment to the human genome (hg 19) was performed using STAR (version 2.5.2b)
Genome_build: hg19
Supplementary_files_format_and_content: Counted reads per gene as raw counts and normalized counts. Normalized counts contain all genes which sum of mapped reads across all samples is greater than one. Normalizing was performed with DESeq2.
|
| |
|
| Submission date |
Mar 06, 2020 |
| Last update date |
Apr 16, 2020 |
| Contact name |
Katrin Kreuzer |
| E-mail(s) |
[email protected]
|
| Organization name |
German Federal Institute for Risk Assessment
|
| Department |
Food Safety
|
| Street address |
Max-Dohrn-Str. 8-10
|
| City |
Berlin |
| ZIP/Postal code |
10589 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE146549 |
Analysis of transcriptomic responses of genotoxic stress in human HepaRG hepatocarcinoma cells |
|
| Relations |
| BioSample |
SAMN14317258 |
| SRA |
SRX7862661 |
