|
| Status |
Public on Jan 12, 2018 |
| Title |
SUM44_wt_repl2 |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast cancer cell line
biomaterial provider: ATCC
cell line: SUM44
estrogen: Yes
antibody: ESR1 (Santa-Cruz sc543)
esr1 mutation: None
|
| Treatment protocol |
LTED cells modeling resistance to an AI were derived from long-term culture in the presence of RPMI1640 medium containing 10% dextran charcoal stripped serum (DCC)
|
| Growth protocol |
cultured in phenol red-free RPMI1640 medium supplemented with 10% FBS and 1 nmol/L estradiol (E2)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked in 1% formaldehyde at room temperature for 10 minutes and then quenched with 125 mmol/L glycine. Samples were then lysed, sonicated, and chromatin was immunoprecipitated by overnight incubation at 4C with ER antibodies prebound with Protein G magnetic dynabeads (Invitrogen). Samples were then washed vigorously with RIPA buffer and reversed crosslinked by an overnight incubation in elution buffer at 65C. DNA was digested with RNase and Proteinase K, purify precipitated with phenol chloroform and eluted in Tris-HCl pH 8.0.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ChIP SUM44 ESR1 wildtype
|
| Data processing |
Reads were aligned to the Human Reference Genome (assembly hg19) using BWA and removing all reads with a quality score <15
Peaks were called using MACS2 (v2.1.0.20150420) 32 with default parameters
Genome_build: Human Reference Genome (assembly hg19)
Supplementary_files_format_and_content: MACS2 excel file output files
|
| |
|
| Submission date |
Jun 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Eugene Schuster |
| E-mail(s) |
[email protected]
|
| Phone |
+442088082619
|
| Organization name |
Institute of Cancer Research
|
| Department |
Breast Cancer Research
|
| Lab |
Endocrinology
|
| Street address |
123 Old Brompton Road
|
| City |
London |
| ZIP/Postal code |
SW7 3RP |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE100074 |
Discovery of naturally occurring ESR1 mutations during acquisition of resistance to endocrine therapy in widely used estrogen receptor positive breast cancer cell lines [ChIP-Seq] |
| GSE100076 |
Discovery of naturally occurring ESR1 mutations during acquisition of resistance to endocrine therapy in widely used estrogen receptor positive breast cancer cell lines |
|
| Relations |
| BioSample |
SAMN07247012 |
| SRA |
SRX2922232 |
