|
| Status |
Public on May 25, 2020 |
| Title |
MK-2206 Patient 4 (IO360 panel) |
| Sample type |
RNA |
| |
|
| Source name |
breast cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary breast cancer
histology: IDC
age: 61
Sex: Female
grade: 2
treatment: MK-2206
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was manually extracted from macrodissected tumor rich areas of surgical specimens of patients treated with MK-2206 (e.g. MK-2206 Patient 1) as well as prospectively enrolled untreated control patients (e.g. Untreated Control 1) and stored at -80C.
|
| Label |
Nanostring bar coding
|
| Label protocol |
Specimens were labeled with decode assignment which was linked to clinical details and treatment received (MK-2206 vs. control)
|
| |
|
| Hybridization protocol |
RNA samples that passed quality and concentration standards were hybridized in a multiplexed to target specific probes and for 20 hours at 65C using 100-400 ng of RNA
|
| Scan protocol |
Following hybridization, the target-probe complexes were purified and immobilized on the nCounter prep station, Digital counts for each gene-specific target RNA were then acquired on the nCounter detection analyzer and normalized to account for differences in tissue mRNA quntiy, as well as slight differences in assay efficiency.
|
| Description |
IO360 Panel
20180202_207795020719_POST-AKT4_04.RCC
|
| Data processing |
For nanoString analysis, data quality assessment, differential expression and statistical comparison was performed by the systems biology data-driven network-based Bayesian inference of drivers (NetBID, https://github.com/jyyulab/NetBID).16 Gene Set Enrichment Analysis (GSEA) was performed using MSigDB (v6.1) and “fgsea” package in R, with default parameters. Multiple comparison analysis was performed using Benjamini-Hochberg method.
|
| |
|
| Submission date |
May 13, 2020 |
| Last update date |
May 25, 2020 |
| Contact name |
Douglas Marks |
| E-mail(s) |
douglaskmarks@gmail.com
|
| Phone |
5166472013
|
| Organization name |
NYU Langone Health
|
| Street address |
120 Mineola Boulevard
|
| City |
Mineola |
| State/province |
NY |
| ZIP/Postal code |
11501 |
| Country |
USA |
| |
|
| Platform ID |
GPL27956 |
| Series (2) |
| GSE150458 |
Akt inhibition with MK-2206 is associated with favorable immune profile changes within the tumor microenvironment of hormone receptor positive, HER2 negative breast cancer [IO360 panel] |
| GSE150512 |
Akt inhibition with MK-2206 is associated with favorable immune profile changes within the tumor microenvironment of hormone receptor positive, HER2 negative breast cancer |
|
