|
| Status |
Public on Aug 07, 2023 |
| Title |
TAMR Decitabine Recovery 2 [EPIC] |
| Sample type |
genomic |
| |
|
| Source name |
TAMR cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Tamoxifen-resistant (TAMR) MCF7 cells
treatment: Decitabine Recovery
replicate: 2
|
| Treatment protocol |
Cells were treated daily with Decitabine (100 nM) for 7 consecutive days and harvested at day 7 (“Decitabine Day 7”). Control cells were cultured for a total of 11 days in normal media and harvested for “Control Early”. For the “Decitabine Recovery” samples, cells were treated daily with Decitabine (100nM) for 7 consecutive days, after which fresh media was added; cells were cultured for 28 additional days and harvested on day 35. Matched control cells were cultured for 35 days in normal media and harvested at day 35 for “Control Late”.
|
| Growth protocol |
Tamoxifen-resistant MCF7 cells (TAMR) were previously generated by the long-term culture of MCF7 cells in phenol red-free RPMI medium containing 10% charcoal-stripped FBS (Gibco) and 4-OH-tamoxifen (1 × 10−7 M; TAM).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Gernomic DNA from cells was isolated using the QIAamp DNA Mini Kit (Qiagen).
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina 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 BeadArray Reader using standard recommended Illumina scanner setting
|
| Data processing |
Raw intensity data (IDAT) files were imported and quality controlled using minfi package (v.1.34.0) (Aryee et al., 2014). Data was then normalised with background correction. To reduce the risk of false discoveries, we removed probes affected for cross-hybridization to multiple locations on the genome or overlapped SNPs, as previously described (Pidsley et al., 2016). Beta (β) values were calculated from unmethylated (U) and methylated (M) signal [M/(U + M + 100)] and ranged from 0 to 1 (0 to 100% methylation). β values of loci whose detection P values were > 0.01 were assigned NA in the output file. To map EPIC arrays to hg38/GRCh38 assembly, all probes were annotated with the EPIC.hg38.manifest.tsv.gz files as described in (Zhou et al., 2017).
|
| |
|
| Submission date |
Nov 01, 2022 |
| Last update date |
Aug 07, 2023 |
| 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 |
GPL21145 |
| Series (2) |
| GSE216986 |
Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions [EPIC] |
| GSE216989 |
Decitabine treatment reveals a functional role of DNA hypomethylation in organising enhancer-promoter interactions |
|
