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Sample GSM4139674 Query DataSets for GSM4139674
Status Public on Oct 26, 2019
Title Glioblastoma 7
Sample type RNA
 
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).
 
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

Data table header descriptions
ID_REF
VALUE SST-RMA signal estimates from Transcriptome Analysis Console software (Thermo)

Data table
ID_REF VALUE
TC01000001.hg.1 5.678070068
TC01000002.hg.1 5.823110104
TC01000003.hg.1 4.677909851
TC01000004.hg.1 6.164700031
TC01000005.hg.1 10.48927975
TC01000006.hg.1 17.78429031
TC01000007.hg.1 16.9101696
TC01000008.hg.1 7.013289928
TC01000009.hg.1 6.095980167
TC01000010.hg.1 5.669469833
TC01000011.hg.1 6.195409775
TC01000012.hg.1 6.907149792
TC01000013.hg.1 14.46490955
TC01000014.hg.1 7.169209957
TC01000015.hg.1 6.855150223
TC01000016.hg.1 7.54610014
TC01000017.hg.1 5.992330074
TC01000018.hg.1 7.492780209
TC01000019.hg.1 7.262829781
TC01000020.hg.1 5.574110031

Total number of rows: 70523

Table truncated, full table size 1930 Kbytes.




Supplementary file Size Download File type/resource
GSM4139674_G7.CEL.gz 21.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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