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Status |
Public on Oct 26, 2019 |
Title |
Glioblastoma 7 |
Sample type |
RNA |
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|
Source name |
Glioblastoma 7
|
Organism |
Homo sapiens |
Characteristics |
tissue: brain tumor type: glioblastoma rsk1 protein group: lo batch: old
|
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).
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|
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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 |
|