|
| Status |
Public on Oct 21, 2022 |
| Title |
Yale Melanoma ITx1_1.7 |
| Sample type |
RNA |
| |
|
| Source name |
Malignant melanoma
|
| Organism |
Homo sapiens |
| Characteristics |
age: 74
bor: PD
pfs_days: 81
pfs_index: 1
long-term benefit: NO
os_days: 446
os_index: 1
itx: IPI+NIVO
prior checkpoint blockade: NO
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 5 μm-thick pretreatment FFPE sections of tumors fixed on positively charged slides using the High Pure FFPET RNA Isolation Kit (Roche) following the manufacturer’s protocols. RNA was quantified using the NanoDrop ND1000 spectrophotometer (Thermo Fisher Scientific).
|
| Label |
biotin
|
| Label protocol |
Per sample, 250 ng of total RNA in a final volume of 5 μl was mixed with a 3′ biotinylated capture probe and a 5′ reporter probe and tagged with a fluorescent barcode from the custom gene expression code set.
|
| |
|
| Hybridization protocol |
Probes and target transcripts were hybridized at 67°C for 16–24 hours per manufacturer’s recommendations.
|
| Scan protocol |
Hybridized samples were run on the NanoString nCounter preparation station using the high-sensitivity protocol, in which excess capture and reporter probes were removed and transcript-specific ternary complexes were immobilized on a streptavidin-coated cartridge. The cartridge was scanned at maximum scan resolution on the nCounter Digital Analyzer
|
| Data processing |
Raw data counts were normalized using the geomean of 10 housekeeping genes included in the nCounter PanCancer IO 360™ Panel and each gene was adjusted based on the average of 2 panel standards across all data. Then, the housekeeper- and panel standard-normalized data were log2 transformed.
|
| |
|
| Submission date |
Oct 16, 2022 |
| Last update date |
Oct 21, 2022 |
| Contact name |
Ioannis Vathiotis |
| E-mail(s) |
ioannis.vathiotis@yale.edu
|
| Organization name |
Yale
|
| Street address |
310 Cedar St
|
| City |
New Haven |
| ZIP/Postal code |
06510 |
| Country |
USA |
| |
|
| Platform ID |
GPL27956 |
| Series (1) |
| GSE215868 |
Baseline gene expression profiling determines long-term benefit to programmed cell death protein 1 axis blockade |
|
