|
| Status |
Public on Apr 06, 2020 |
| Title |
Patient78_Pretreatment [FFP17.009547] |
| Sample type |
RNA |
| |
|
| Source name |
Patientsample_brca_NCT00738777
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: breast cancer patient
subject id: Patient78
treatment: Pretreatment
tissue/sample type: FFPE tumor
batch: Batch SJ
|
| Treatment protocol |
Gene expression of primary breast cancers from patients before and after neo-adjuvant Tamoxifen treatment
FFPE sections of patient tumor material (10 x CF 5u gelcoat per sample) were sent to Agendia Inc.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Qiagen RNeasy microkit according to manufacturer's specifications.
|
| Label |
Cy3
|
| Label protocol |
RNA was amplified and labeled using the lQuickAmp Labeling kit (Agilent).
|
| |
|
| Hybridization protocol |
200 ng fluorescent labeled RNA was hybridized to custom Agilent arrays (4x44k arrays).
|
| Scan protocol |
Agilent Technologies Scanner G2505B, Agilent Scan Control Version A.7.0.3.
|
| Data processing |
Feature Extraction software v11.5.1.1 was used to quantify fluorescent intensities, custom script were used for raw data extraction and those values were normalized by 75th percentile normalisation using DataPrint software v1.15, all by Agendia Inc. Downstream data processing was subsequently done at the Netherlands Cancer Institute, by missing data impution with knn=10 and batch correction for date of RNA extraction using ComBat from the R package sva, using all available patient material from the trial (ClinicalTrials.gov Identifier: NCT00738777). Here we deposited samples used for the Tamoxifen focused analysis described in the cited paper.
|
| |
|
| Submission date |
Mar 20, 2020 |
| Last update date |
Apr 07, 2020 |
| Contact name |
Wilbert Zwart |
| E-mail(s) |
w.zwart@nki.nl
|
| Organization name |
Netherlands Cancer Institute
|
| Department |
Oncogenomics
|
| Lab |
Zwart lab
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| State/province |
Noord-Holland |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL28292 |
| Series (1) |
| GSE147271 |
Gene expression of primary breast cancers from patients before and after neo-adjuvant Tamoxifen treatment |
|
