|
| Status |
Public on Dec 14, 2023 |
| Title |
35_PNF |
| Sample type |
RNA |
| |
|
| Source name |
FFPE tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: IU12_M
diagnosis: PNF
age at surgery: 19
Sex: Female
race/ethnicity: Hispanic or Latino
nf1 diagnosis: Yes
family history of nf1: Yes
location: Right axilla/shoulder/chest wall
biopsy vs surgical resection: Resection
procedure (1st, 2nd, etc.): 1st
primary vs metastatic: Primary
prior chemotherapy: Ifos/Doxo
prior radiation (dose if known): Yes (45 Gy)
contiguous with mpnst: Yes
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Formalin fixed paraffin embedded (FFPE) tissues were microdissected from 5 µm thick sections on freshly cut slides.
Total RNA was extracted using a RNeasy FFPE Kit (Qiagen). RNA concentration and fragmentation index were quantified on an Agilent bioanalyzer.
Fragmentation index (percent greater than 200 bp) was used to normalize the loading of 50 ng total input RNA in a final volume of 5 µL with the capture probe set.
|
| Label |
NA
|
| Label protocol |
NA
|
| |
|
| Hybridization protocol |
Probes and target transcripts were hybridized for 20 hours at 65°C per the manufacturer's recommendations.
|
| Scan protocol |
NA
|
| Description |
batch_3
|
| Data processing |
Hybridized samples were loaded into a nCounter cartridge and quantified on the nCounter® Sprint Profiler
Quality control, normalization, differential expression and pathway analysis were performed using nSolver Advanced Analysis Software (version 4.0, NanoString Technologies, Inc.) .
|
| |
|
| Submission date |
Jul 28, 2023 |
| Last update date |
Dec 14, 2023 |
| Contact name |
Steven Rhodes |
| E-mail(s) |
sdrhodes@iu.edu
|
| Organization name |
Indiana University
|
| Street address |
1044 W. Walnut St.; Bldg R4, Rm 325
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL32069 |
| Series (1) |
| GSE239561 |
Spatial gene expression profiling unveils immuno-oncogenic programs of NF1-associated peripheral nerve sheath tumor progression |
|
