|
| Status |
Public on Oct 26, 2019 |
| Title |
Glioblastoma 2 |
| Sample type |
RNA |
| |
|
| Source name |
Glioblastoma 2
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: brain
tumor type: glioblastoma
rsk1 protein group: lo
batch: new
|
| Treatment protocol |
Formalin-fixed, paraffin-embedded (FFPE)
|
| Growth protocol |
glioblastoma samples
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA from the 30 glioblastoma (GBM) samples from the A.C.Camargo Cancer Center (ACCCC) cohort was extracted from formalin-fixed, paraffin-embedded (FFPE) slices using the ReliaPrep™ FFPE Total RNA Miniprep System (Promega)
|
| Label |
3' IVT
|
| Label protocol |
3' IVT Labeling Kit (Thermo)
|
| |
|
| Hybridization protocol |
SensationPlus™ FFPE Amplification and WT Labeling Kit
|
| Scan protocol |
GeneChip® Expression Wash, Stain and Scan
|
| Description |
RSK1 protein groups were defined based on RSK1 protein levels and survival
|
| Data processing |
Primary processing (matrix submitted to GEO): The CEL files were normalized and summarized at the gene level using SST-RMA algorithm from the Transcriptome Analysis Console software (Thermo). Further processing: Normalized expression and DABG (detection above background) values were retrieved from the CHP files using the affxparser package. Five of the 30 FFPE-blocks were newer and a batch effect was observed for them. Thus, ComBat algorithm was used to remove batch effects (Leek et al., 2012). Transcript clusters with DABG ≥ 0.05 for all of the samples were excluded. Data were annotated according to the hta20transcriptcluster.db package in R. Only transcript clusters with a corresponding RefSeq ID for protein (“NP”) were kept, and transcript clusters for the same gene were collapsed (based on max intensity) using the WGCNA package (Langfelder and Horvath, 2008).
|
| |
|
| Submission date |
Oct 25, 2019 |
| Last update date |
Oct 26, 2019 |
| Contact name |
Martin - Roffe |
| E-mail(s) |
MRoffe@cheo.on.ca
|
| Organization name |
CHEO Research Institute
|
| Street address |
401 Smyth Rd
|
| City |
Ottawa |
| State/province |
ON |
| ZIP/Postal code |
K1H 5B2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL17586 |
| Series (1) |
| GSE139380 |
Aberrant expression of RSK1 characterizes high-grade gliomas with immune infiltration |
|
