|
| Status |
Public on Dec 11, 2019 |
| Title |
WGBS FASR |
| 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 |
Library preparation and indexing were carried out as described in the CEGX TruMethyl WG user guide v2 wih minor improvements as described in Nair et al., 2018.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
ClarkLab_FASR_WGBS
|
| Data processing |
Sequencing reads from WGBS data were aligned to the human genome using version 1.2 of an internally developed pipeline Meth10X. It is publicly available and can be downloaded from https://github.com/luuloi/Meth10X (Nair et al., 2018). The pipeline backbone is built based on workflow control Bpipe (Sadedin SP at el. 2012) version 0.9.9.2 which mainly help to make automation, parallelism, restarting jobs and integration with cluster resource managers easier following the pipeline structure of P3BSseq (Luu PL, et al., 2017). Meth10X takes raw bisulphite reads in fastq files as inputs and produces a html report of all necessary metrics of bisulphite quality control and a tsv file of DNA methylation of 28 million CpG as rows and samples as columns. Briefly, adaptor sequences were removed using in-house bash script in paired end mode following prep kit guide. Bwa-meth verion 0.20 (https://github.com/brentp/bwa-meth) was then used to align reads to hg38 using bwa version 0.7.13 (https://github.com/lh3/bwa). The generated bam files are merged and marked duplication by Picard tools 2.3.0 (http://broadinstitute.github.io/picard). The merged bam files are checked with Qualimap 2.2.1 (Konstantin Okonechnikov at el. 2015) for quality as well as all metrics of WGBS. MethylDackel (https://github.com/dpryan79/MethylDackel) and Biscuit (https://github.com/zwdzwd/biscuit) are used to call DNA methylation and SNP. Samtools version 1.2 (Li H.et al. 2009) is used to manipulate bam files and all the plots are done with ggplot2 in R (H. Wickham. 2009).
Genome_build: hg38
Supplementary_files_format_and_content: BigWig file containing counts of methylated (C) and coverage (cov, methylated Cs + unmethylated Ts) at each CpG site assayed; Bed file containing DMRs identified using Bisulfighter (Saito et al., 2014).
|
| |
|
| 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
|
| Lab |
Epigenetics Research Laboratory
|
| Street address |
384 Victoria Street
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE118714 |
Epigenetic reprogramming at estrogen-receptor binding sites alters the 3D chromatin landscape in endocrine resistant breast cancer [WGBS] |
| GSE118716 |
Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine resistant breast cancer |
|
| Relations |
| BioSample |
SAMN09848858 |
| SRA |
SRX4565005 |
