|
| Status |
Public on Jul 17, 2020 |
| Title |
T47D_WT_0month_biolrep2-techrep1 |
| Sample type |
genomic |
| |
|
| Source name |
T47D, WT, 0 month
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T47D
treatment: WT
time: 0 months
biological_replicate: 2
technical_replicate: 1
gender: Female
|
| Treatment protocol |
Parental sensitive T47D cells were cultured for 7 months (biological replicate 1) and 5 months (biological replicate 2) in the presence of 100nM tamoxifen or in estrogen deprivation to obtain T47D-TAMR and T47D-LTED respectively. The cells were passaged when they reached 80% confluency or reseeded in a new dish if they were not reaching confluency for more than 4 weeks. In this case, the medium was changed every week to ensure availability of nutrient. Two independent resistance acquisitions were performed in parallel therefore generating two replicates of resistant cell lines.
|
| Growth protocol |
Parental T47D breast cancer cells were obtained from ATCC (HTB-133). Cell lines were regularly sent for cell line authentication to Multiplexion GmbH and tested for mycoplasma contamination. The cell lines were cultured in the respective media (WT: DMEM + 10% FBS + 1% P/S + 10-8M 17-ß-estradiol (E2);TAMR: DMEM + 10% FBS + 1% P/S + 100nM TAM (TAM); LTED: DMEM - phenol red + 10% charcoal stripped FBS + 1% P/S + 1% Glutamine + 1% Sodium Pyruvate), and incubated at 37 degrees Celsius with 5% CO2 in a humidified atmosphere.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was isolated by standard procedures
|
| Label |
Cy3,Cy5
|
| Label protocol |
Standard Illumina labelling protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting
|
| Description |
Infinium MethylationEpic
WT_0m_2_1
201533480052_R01C01
|
| Data processing |
Pre-processing was performed using the R/Bioconductor package minfi. Detection p-values were calculated for each methylation probe. Data were normalized using functional normalization using the function preprocessFunnorm in the minfi package.
|
| |
|
| Submission date |
Jul 17, 2020 |
| Last update date |
Jul 17, 2020 |
| Contact name |
Perry D Moerland |
| E-mail(s) |
[email protected]
|
| Organization name |
Amsterdam UMC
|
| Department |
Epidemiology and Data Science
|
| Lab |
Bioinformatics Laboratory
|
| Street address |
Meibergdreef 9
|
| City |
Amsterdam |
| ZIP/Postal code |
1105AZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE154626 |
Time-resolved DNA methylation profiling of endocrine resistance in the T47D luminal A breast cancer cell line |
|
