|
| Status |
Public on Dec 11, 2019 |
| Title |
TAMR_CTCF_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
TAMR
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
cell type: breast cancer cells
resistant phynotype: tamoxifen-resistant
chip antibody: CTCF millipore 07-729
|
| 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 |
Nuclei were purified after formaldehyde crosslinking, collected and resuspended in SDS Lysis buffer before sonication. Chromatin was sonicated to generate a majority of fragments between 200 and 600 bp. 10µg of each antibody was used per ChIP.
Libraries for ChIP-Seq were prepared following Illumina protocols. The resulting libraries were sequenced on the Illumina HiSeq 2000 platform configured for 50bp single-end reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
USC20140314_TAMR_CTCF
|
| Data processing |
ChIP-seq reads were aligned to hg38 using bowtie v2.2.4 allowing up to 3 mismatches, discarding ambiguous and clonal reads. Peaks were called with Macs2 version 2.0.10.
Genome_build: hg38
Supplementary_files_format_and_content: Bigbed files were generated using Macs2 version 2.0.10.
|
| |
|
| 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 |
GPL11154 |
| Series (2) |
| GSE118711 |
Epigenetic reprogramming at estrogen-receptor binding sites alters the 3D chromatin landscape in endocrine resistant breast cancer [ChIP-seq] |
| GSE118716 |
Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine resistant breast cancer |
|
| Relations |
| BioSample |
SAMN09848841 |
| SRA |
SRX4564976 |
