|
| Status |
Public on Jan 27, 2021 |
| Title |
HaCaT_SM [WGS] |
| Sample type |
SRA |
| |
|
| Source name |
SM-resistant HaCaT cell line
|
| Organism |
Homo sapiens |
| Characteristics |
exposure (yes/no): yes
cell line: human keratinocyte cell line
|
| Growth protocol |
HaCaT cells were kindly provided by Prof. Dr. N. Fusenig (German Cancer Research Center, Heidelberg, Germany) and cultivated in Dulbecco’s Modified Eagle Medium supplemented with glutamine and 10 % fetal bovine serum (Gibco, Carlsbad, CA). Cells were maintained at 37 °C and 5 % CO2 in a humidified atmosphere. For cell passaging, HaCaT were detached with 0.05 % trypsin in 1 mM EDTA (Gibco, Carlsbad, CA) for 5 min and reseeded in fresh culture medium twice a week.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
2x 125 bp reads were generated for HaCaT and HaCaT/SM on a HiSeq2500 (Illumina).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: WGS
Whole genome sequencing and variant calling: Adapter sequences and low quality bases (Phred <20) were clipped off by means of Trimmomatic. Reads < 40bp after clipping were excluded from further analysis.
|
| |
|
| Submission date |
Dec 01, 2020 |
| Last update date |
Jan 27, 2021 |
| Contact name |
Hanns Leonhard Kaatsch |
| E-mail(s) |
hannsleonhardkaatsch@bundeswehr.org
|
| Organization name |
Bundeswehr Institute of Radiobiology
|
| Street address |
Neuherbergstraße 11
|
| City |
Munich |
| ZIP/Postal code |
80937 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE162401 |
Genomic adaptation and mutational patterns in a HaCaT subline resistant to alkylating agents and ionizing radiation [WGS] |
| GSE162646 |
Genomic adaptation and mutational patterns in a HaCaT subline resistant to alkylating agents and ionizing radiation |
|
| Relations |
| BioSample |
SAMN16968112 |
