|
| Status |
Public on Jul 29, 2020 |
| Title |
WHI11-Untreated [SG186-WHIM11-GFP-Luc-Ctrl4] |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Human universal, Stratagene, Human Reference B
|
| Organism |
Homo sapiens |
| Characteristics |
reference: High-quality total RNA. Comprised of 10 different cell lines for broad gene coverage on human microarrays
|
| Treatment protocol |
Tumors treated with BLU9931 (0.6g/Kg/day) or Lapatinib (0.22g/kg/day) for 18 days
|
| Growth protocol |
PDX WHIM11 tumors were engrafted in the mammary fat pad of NSG mice by subcutaneous injection of 1.0 × 10^6 cells in RPMI:Matrigel (1:1) in a total volume of 200 μl
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor tissue was disrupted using roto-stator homogenization. RNA was isolated using the RNeasy Mini Kit (QUIAGEN) according to manufacturer protocol. Isolated RNA was quantified using a NanoDrop® Spectrophotometer.
|
| Label |
Cy3
|
| Label protocol |
1 ug of Total RNA was amplified and labeled using Agilent’s Low RNA Input Linear Amplification Kit. RNA labeling tumor (Cy5 CTP) and reference (Cy3 CTP) were measured by NanoDrop
|
| |
|
| Channel 2 |
| Source name |
Patient derived breast tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: WHIM11 tumor
agent: Untreated
|
| Treatment protocol |
Tumors treated with BLU9931 (0.6g/Kg/day) or Lapatinib (0.22g/kg/day) for 18 days
|
| Growth protocol |
PDX WHIM11 tumors were engrafted in the mammary fat pad of NSG mice by subcutaneous injection of 1.0 × 10^6 cells in RPMI:Matrigel (1:1) in a total volume of 200 μl
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor tissue was disrupted using roto-stator homogenization. RNA was isolated using the RNeasy Mini Kit (QUIAGEN) according to manufacturer protocol. Isolated RNA was quantified using a NanoDrop® Spectrophotometer.
|
| Label |
Cy5
|
| Label protocol |
1 ug of Total RNA was amplified and labeled using Agilent’s Low RNA Input Linear Amplification Kit. RNA labeling tumor (Cy5 CTP) and reference (Cy3 CTP) were measured by NanoDrop
|
| |
|
| |
| Hybridization protocol |
Labeled tumor and reference RNA were mixed and co-hybridized overnight on Agilent custom 44K whole genome microarrays
|
| Scan protocol |
Microarrays were scanned on an Agilent G2565CA Microarray Scanner System, read it with the scan Control Software 8.5.1 and data was extracted with Feature Extraction Software 11.5.1
|
| Data processing |
Microarray raw data were uploaded into the UNC Microarray Database and Lowess normalization was performed on the Cy3 and Cy5 channels
|
| |
|
| Submission date |
Feb 04, 2019 |
| Last update date |
Jul 30, 2020 |
| Contact name |
Charles M. Perou |
| E-mail(s) |
[email protected]
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center
|
| Street address |
12-044 Lineberger Comprehensive Cancer Center CB# 7295
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7264 |
| Country |
USA |
| |
|
| Platform ID |
GPL20311 |
| Series (2) |
| GSE126037 |
FGFR4 is a key regulator of tumor subtype differentiation in luminal breast cancer and metastatic disease [set 2] |
| GSE126038 |
FGFR4 is a key regulator of tumor subtype differentiation in luminal breast cancer and metastatic disease |
|
