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Sample GSM1130277 Query DataSets for GSM1130277
Status Public on Jan 31, 2014
Title hcc_052 [tumor from HCC patient]
Sample type RNA
 
Source name hcc_052
Organism Homo sapiens
Characteristics disease state: hepatocellular carcinoma
tissue: AS-FFPE tumor
%p-call: 0.215561143629947
inter-sample correlation: 0.578593129823743
prediction in as-ffpe: S1 (HCC subclass: aberrant activation of the TGF-beta/WNT signaling pathways)
prediction confidence p-value in as-ffpe: 0.734421859
prediction in as-ffpe (%p-call>20%): S1 (HCC subclass: aberrant activation of the TGF-beta/WNT signaling pathways)
prediction confidence p-value in as-ffpe (%p-call>20%): 0.888037321
prediction in fc-ffpe: S1 (HCC subclass: aberrant activation of the TGF-beta/WNT signaling pathways)
prediction confidence p-value in fc-ffpe: 0.000333222
geo accession of fc-ffpe profile: GSM256460
Treatment protocol FFPE tissue sections (10 micron-thick) sliced from 5~16-year-old FFPE blocks and archived for 6~7 years on glass slide
Growth protocol na
Extracted molecule total RNA
Extraction protocol RNA was isolated with Triazol reagent (Invitrogen) according to manufacturer’s protocol.
Label biotin
Label protocol Refer to the Illumina beadarray Assay System Manual
 
Hybridization protocol Refer to the Illumina beadarray Assay System Manual
Scan protocol Refer to the Illumina beadarray Assay System Manual
Description Sample name: hcc_052
Data processing For each probe, replicated mesurements (beads) were averaged after removing outliers by Genome Studio software v.3 (Illumina). Data were were then normalized using qubic spline algorithm implemented in GenePattern Illumina normalizer module (www.broadinstitute.org/genepattern) after setting a floor value of 1.
 
Submission date Apr 27, 2013
Last update date Jan 31, 2014
Contact name Yujin Hoshida
Organization name University of Texas Southwestern Medical Center
Street address 5323 Harry Hines Blvd
City Dallas
State/province TX
ZIP/Postal code 75390
Country USA
 
Platform ID GPL13369
Series (2)
GSE46444 Gene-expression profiles of archived section of formalin-fixed paraffin-embedded (AS-FFPE) liver and tumor tissues from hepatocellular carcinoma patients
GSE47595 Gene-expression profiles of archived section of formalin-fixed paraffin-embedded (AS-FFPE) liver and tumor tissues from hepatocellular carcinoma patients (Illumina and Nanostring)
Relations
Affiliated with GSM256460

Data table header descriptions
ID_REF
VALUE Normalized signal intensities

Data table
ID_REF VALUE
ILMN_1762337 53.34592807
ILMN_2055271 450.3520449
ILMN_1736007 60.16330338
ILMN_2383229 38.63781909
ILMN_1806310 484.930052
ILMN_1779670 86.37479256
ILMN_1653355 42.39902372
ILMN_1717783 420.4128722
ILMN_1705025 74.87524286
ILMN_1814316 120.943104
ILMN_2359168 94.34299915
ILMN_1731507 35.35107031
ILMN_1787689 107.0993628
ILMN_3241953 41.53086746
ILMN_1745607 4839.403315
ILMN_2136495 67.11689732
ILMN_1668111 42.77875071
ILMN_2295559 38.01600665
ILMN_1735045 436.7654514
ILMN_1680754 260.4493332

Total number of rows: 47323

Table truncated, full table size 1150 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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