|
| Status |
Public on Nov 09, 2023 |
| Title |
genomic DNA from HCI-010 (TNBC PDX) |
| Sample type |
genomic |
| |
|
| Source name |
breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
pdx model id: HCI-010
|
| Treatment protocol |
na
|
| Growth protocol |
Tumors were induced by bilateral orthotopic mammary fat pad injection of 2 × 10^6 PDX cells suspended in 50 μl total volume of 50% DMEM media and 50% of Matrigel
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was extracted and purified from samples using Qiagen ALLPrep according to standard instructions
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
hybridisation to Illumina Infinium Human Methylation450K array was performed using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
genomic DNA from HCI-010
|
| Data processing |
Data were preprocessed using the R package minfi {PMID: 24478339}, using the function preprocessIllumina with default parameters.
|
| |
|
| Submission date |
May 11, 2022 |
| Last update date |
Nov 09, 2023 |
| Contact name |
Kornelia Polyak |
| E-mail(s) |
kornelia_polyak@dfci.harvard.edu
|
| Phone |
617-632-2106
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Polyak
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE202775 |
Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer (PDX Methylation) |
| GSE202776 |
Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer |
|
