|
| Status |
Public on Nov 18, 2024 |
| Title |
380_primary |
| Sample type |
RNA |
| |
|
| Source name |
GMB
|
| Organism |
Homo sapiens |
| Characteristics |
primary_recurrent: primary
relapse time (d): 1260
patientid: 380
|
| Growth protocol |
GBM tissue samples were collected directly in the operating theater during primary (first) and recurrent (second) surgeries and immediately stored in RNAlater stabilization solution (Thermo Fisher Scientific, USA) on ice and stored at -80 °C until further use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors were mechanically dissociated in lysis buffer using a syringe equipped with a 23G needle, and total RNA was extracted using the AllPrep DNA/RNA/protein mini Kit (Qiagen, USA, Cat. No. / ID: 80004) according to the manufacturer’s protocol
|
| Label |
Iso360 panel
|
| Label protocol |
slides were stained using a mixture of conjugated antibodies for identification of tissue morphology: anti-GFAP-594 (Novus Biologicals, NBP2-33184DL594; 1:1000) and anti-CD64 (purified with Abcam purification kit (ab102784) and conjugated with AlexaFluor647 (ab269235); 1:50) for the labeling of tumor cells and myeloid cells, respectively. In addition, Syto83 was used for DNA labeling (ThermoFisher Scientific, USA, 1:25)
|
| |
|
| Hybridization protocol |
Gene expression code sets were hybridized in a thermocycler for 18 h at 65 °C prior to being processed in the nCounter Prep Station (Nanostring Technologies, USA)
|
| Scan protocol |
Gene expression was assessed using the nCounter PanCancer IO 360 panel comprising 770 genes (including 10 house-keeping genes, NanoString Technologies, Seattle, WA), using 50 ng of total RNA per tumor sample
|
| Description |
NS_IO_360_v1.0
|
| Data processing |
each panel was normalised separately using the limma package and between-samples cyclic loess normalization
The matrix table displays log2 transformed cpm
|
| |
|
| Submission date |
Feb 01, 2024 |
| Last update date |
Nov 18, 2024 |
| Contact name |
Sabrina Annie Hogan |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Basel
|
| Street address |
Hebelstrasse 20
|
| City |
Basel |
| ZIP/Postal code |
4031 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL32130 |
| Series (2) |
| GSE254874 |
Multidimensional analysis of patient-matched primary and recurrent glioblastoma identifies microglial FCGR1A (CD64) and other FCGRs as contributors of tumor recurrence [NS_IO_360_v1.0] |
| GSE254875 |
Multidimensional analysis of patient-matched primary and recurrent glioblastoma identifies microglial FCGR1A (CD64) and other FCGRs as contributors of tumor recurrence |
|
