|
| Status |
Public on Jan 29, 2023 |
| Title |
Patient 50 |
| Sample type |
RNA |
| |
|
| Source name |
Medulloblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
age years: 44.1
dead status: 1
metastasis: Yes
gender: M
subgroup: SHH
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation and quantification were performed using the RNeasy Mini Kit (Qiagen, Venlo, The Netherlands) and NanoDroPVR 2000 (Thermo Scientific, Waltham).
|
| Label |
Capture and reporter probes
|
| Label protocol |
Capture and reporter probes were used for 21 hours to label the mRNA.
|
| |
|
| Hybridization protocol |
All washing steps and the probe-mRNA complexes fixation into the cartridge were performed automatically in the prep station of the nCounter® PrepStation (NanoString). No post-process actions are needed since all the probes were already marked with specific color sequences.
|
| Scan protocol |
The cartridges containing immobilized reporter complexes were transferred to nCounter® Digital Analyzer (NanoString) and analyzed using the PanCancer Immune Profiling Panel (NanoString Technologies, Inc., Seattle, WA)
|
| Description |
Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
80-SHH
|
| Data processing |
ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library
|
| |
|
| Submission date |
Jan 24, 2023 |
| Last update date |
Jan 29, 2023 |
| Contact name |
Rui Pedro Ferreira Marques |
| E-mail(s) |
pg45863@alunos.uminho.pt
|
| Organization name |
School of Medicine, University of Minho
|
| Department |
Life and Health Sciences Institute
|
| Lab |
BiTCancer
|
| Street address |
Campus de Gualtar
|
| City |
Braga |
| ZIP/Postal code |
4710-057 |
| Country |
Portugal |
| |
|
| Platform ID |
GPL32232 |
| Series (1) |
| GSE223606 |
Nanostring analysis of medulloblastoma samples using the PanCancer Immune Profile Nanostring Panel |
|
