|
| Status |
Public on Jul 31, 2016 |
| Title |
253949423926_2_2 |
| Sample type |
RNA |
| |
|
| Source name |
S1057-00014 R1
|
| Organism |
Homo sapiens |
| Characteristics |
patientid: 11
tumor type: Breast
primary/metastatic biopsy: Metastatic
biopsy site: Liver
best response: PR
rnaqc_pass: Fail
|
| Treatment protocol |
27 pre-treatment FFPE biopsy samples from 16 unique patients in our MK2206 phase 1b trial collected and sent for gene expression profiling.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed by Almac Diagnostics. RNA was isolated using the Ambion RecoverAll Extraction Kit using an optimised Almac procedure.
|
| Label |
Cy3
|
| Label protocol |
RNA labeling and hybridization was performed by LabCorp. Extracted RNA was labeled using the Sigma WTA kit and Agilent tag labeling protocol as per manufacturer's instruction.
|
| |
|
| Hybridization protocol |
Cy3-labeled cRNA was hybridized to Agilent HD arrays containing ~60K probes (Agilent-039494) as per manufacturer's protocol.
|
| Scan protocol |
Slides were scanned after washing on Agilent DNA Microarray scanner (G2505C) using one color scan setting
|
| Description |
Gene expression from patient sample in MK2206 phase 1b study
|
| Data processing |
For each array, the green channel mean (gMean) signal was log2-tranformed and centered within array to its 75th quantile as per manufacturer’s data processing recommendations. A fixed value of 9.5 was then added to avoid negative values
|
| |
|
| Submission date |
Nov 17, 2015 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Christina Yau |
| E-mail(s) |
cyau@buckinstitute.org
|
| Phone |
415-209-2248
|
| Organization name |
Buck Institute of Age Research
|
| Lab |
Benz Lab
|
| Street address |
8001 Redwood Blvd
|
| City |
Novato |
| State/province |
CA |
| ZIP/Postal code |
94945 |
| Country |
USA |
| |
|
| Platform ID |
GPL16699 |
| Series (1) |
| GSE75087 |
A phase 1b study of the Akt-inhibitor MK-2206 in combination with weekly paclitaxel and trastuzumab in patients with advanced HER2-overexpressing solid tumor malignancies |
|
| Relations |
| Reanalyzed by |
GSE113533 |
