|
| Status |
Public on Dec 11, 2019 |
| Title |
FASR_WGS |
| Sample type |
SRA |
| |
|
| Source name |
FASR
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
cell type: breast cancer cells
resistance phynotype: fulvestrant-resistant
|
| Growth protocol |
MCF7 breast cancer cells, and the corresponding endocrine resistant sub cell lines were kindly given to our laboratory by Dr Julia Gee (Cardiff University, UK). MCF7 cells were maintained in RPMI-1640 based medium containing 5% (v/v) fetal calf serum (FCS). Tamoxifen-resistant MCF7 (TAMR) cells were generated by the long-term culture of MCF7 cells in phenol-red-free RPMI medium containing 5% charcoal stripped FCS and 4-OH-tamoxifen (1×10－7 M) (TAM). Fulvestrant-resistant MCF7 (FASR) cells were generated by the long-term culture of MCF7 cells in phenol-red-free RPMI medium containing 5% charcoal stripped FCS and fulvestrant (1×10－7 M) (FAS). Endocrine resistant sub lines were established and characterised following 6 months endocrine challenge. All cell lines were authenticated by short-tandem repeat (STR) profiling (Cell Bank, Australia) and cultured for less than 6 months after authentication.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extracted from cell lines was used as a starting material for the Nextera TruSeq Library Preparation with PCR amplification. Each sample underwent paired-end (2 x 150bp) sequencing on Illumina HiSeq X Ten instrument generating around 35x coverage per sample.
Whole Genome Sequencing; Nextera TruSeq
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
ClarkLab_FASR_WGS
|
| Data processing |
Sequenced reads were aligned to human reference genome hg38 using bwa-mem v.0.7.9 and the GATK pipeline v.3.5 was used to identify duplicate reads, perform local re-alignment at indels, base quality score recalibration. Mapping statistics were calculated using QualiMap v.2.1.3.
Genome_build: hg38
Supplementary_files_format_and_content: vcf file containing copy number change data obtained using lumpy-sv v.0.2.4
|
| |
|
| Submission date |
Aug 17, 2018 |
| Last update date |
Dec 13, 2019 |
| Contact name |
Joanna Achinger-Kawecka |
| E-mail(s) |
j.achinger@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Street address |
384 Victoria Street
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE118715 |
Epigenetic reprogramming at estrogen-receptor binding sites alters the 3D chromatin landscape in endocrine resistant breast cancer [WGS] |
| GSE118716 |
Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine resistant breast cancer |
|
| Relations |
| BioSample |
SAMN09848853 |
| SRA |
SRX4565002 |
