|
| Status |
Public on Dec 12, 2021 |
| Title |
HCI-005 Vehicle 2_methylation |
| Sample type |
genomic |
| |
|
| Source name |
HCI-005 Vehicle tumour
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast cancer PDX model HCI-005
treatment: Vehicle
replicate: 2
|
| Treatment protocol |
Mice were randomly assigned to treatment groups and treated for 5 days with either a vehicle or Decitabine.
|
| Growth protocol |
A single patient-derived tumor tissue was divided and implanted into the 4th inguinal mammary gland of 6-week-old female NOD-SCID-IL2γR-/- (NSG) mice. Where relevant (PDX model HCI-005), mice were also subcutaneously implanted with an E2 pellet.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Gernomic DNA from Decitabine-treated and Vehicle tumours from two PDX models (GAR15-13D and HCI-005) was isolated from snap-frozen tumour samples 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 |
Mar 29, 2021 |
| Last update date |
Dec 12, 2021 |
| Contact name |
Joanna Achinger-Kawecka |
| E-mail(s) |
[email protected]
|
| Organization name |
South Australian Immunogenomics Cancer Institute
|
| Street address |
AHMS Building, North Terrace
|
| City |
Adelaide |
| State/province |
SA |
| ZIP/Postal code |
5005 |
| Country |
Australia |
| |
|
| Platform ID |
GPL21145 |
| Series (2) |
| GSE171069 |
Epigenetic therapy suppresses tumour growth by rewiring ER-mediated long-range chromatin interactions in ER+ endocrine-resistant breast cancer [methylation HCI-005] |
| GSE171074 |
The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer |
|
