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Sample GSM864173 Query DataSets for GSM864173
Status Public on Feb 24, 2012
Title S05-21206
Sample type RNA
 
Source name FFPE block, diffuse astrocytic glioma
Organism Homo sapiens
Characteristics tumor type: diffuse astrocytic glioma
who grade: II
subclass: EPL
idh mut status: mut
pten methylation: M
cdkn2a methylation: NA
tp53 seq: NA
pten del: No
pdgfra ihc: +
p53 ihc: -
p-pras40 ihc: -
egfr amp: NA
Growth protocol Formalin-fixed parrafin-embedded tissue blocks
Extracted molecule total RNA
Extraction protocol Samples were extracted using the miRNEASY FFPE kit from Qiagen and quality was assessed by RPL13a RT-PCR
Label biotin
Label protocol Following Illumina standard protocol, 300ng RNA  were converted to cDNA through reverse transcription reaction with biotinylated primers. The biotinylated cDNA is then annealed to assay oligonucleotides (oligos), and bound to streptavidin conjugated paramagnetic particles (SA‐PMPs)
 
Hybridization protocol After the oligo hybridization, mis‐hybridized and non‐hybridized oligos are washed away. The hybridized oligos are then extended and ligated. These products form a synthetic template that is transferred to a PCR reaction containing a fluorescently labeled primer
Scan protocol Standard Illumina scanning protocol
Description FFPE material/DASL processed
Data processing The data were analyzed with GenomeStudio using Illumina default analysis settings. Gene level data was obtained by average the probe level data for each gene. The data were then quantile normalized in Partek
 
Submission date Jan 19, 2012
Last update date Feb 24, 2012
Contact name Jason Huse
E-mail(s) husej@mskcc.org
Organization name Memorial Sloan-Kettering Cancer Center
Street address 408 E 69th St. (Z701)
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL14951
Series (1)
GSE35158 Expression profiling of lower-grade diffuse astrocytic glioma

Data table header descriptions
ID_REF
VALUE Log2 values, quantile normalization

Data table
ID_REF VALUE
ILMN_1762337 7.5268
ILMN_2055271 6.62549
ILMN_1779670 6.88211
ILMN_1717783 7.3322
ILMN_1787689 6.99847
ILMN_3241953 7.00016
ILMN_1745607 6.95512
ILMN_2136495 7.35455
ILMN_2295559 6.94392
ILMN_1735045 7.69466
ILMN_1680754 6.9944
ILMN_1673870 6.87859
ILMN_1755321 7.76972
ILMN_1698554 9.45099
ILMN_1760414 7.02023
ILMN_1676336 7.29375
ILMN_1752884 7.22438
ILMN_1668851 6.62241
ILMN_2357031 7.46507
ILMN_3237396 6.71174

Total number of rows: 20792

Table truncated, full table size 424 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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