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Sample GSM1130298 Query DataSets for GSM1130298
Status Public on Jan 31, 2014
Title hcc_083 [tumor from HCC patient]
Sample type RNA
 
Source name hcc_083
Organism Homo sapiens
Characteristics disease state: hepatocellular carcinoma
tissue: AS-FFPE tumor
%p-call: 0.383365382583522
inter-sample correlation: 0.8158629286465
prediction in as-ffpe: S3 (HCC subclass: hepatocyte differentiation)
prediction confidence p-value in as-ffpe: 0.000333222
prediction in as-ffpe (%p-call>20%): S3 (HCC subclass: hepatocyte differentiation)
prediction confidence p-value in as-ffpe (%p-call>20%): 0.000333222
prediction in fc-ffpe: S3 (HCC subclass: hepatocyte differentiation)
prediction confidence p-value in fc-ffpe: 0.000333222
geo accession of fc-ffpe profile: GSM256484
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_083
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 GSM256484

Data table header descriptions
ID_REF
VALUE Normalized signal intensities

Data table
ID_REF VALUE
ILMN_1762337 140.3411515
ILMN_2055271 176.4461087
ILMN_1736007 52.5534753
ILMN_2383229 606.1846987
ILMN_1806310 2864.291134
ILMN_1779670 1066.977677
ILMN_1653355 54.63888473
ILMN_1717783 108.5216665
ILMN_1705025 44.36662044
ILMN_1814316 2735.84782
ILMN_2359168 3339.413122
ILMN_1731507 39.04011143
ILMN_1787689 111.142269
ILMN_3241953 214.5832772
ILMN_1745607 11894.30373
ILMN_2136495 39.64738171
ILMN_1668111 379.0695713
ILMN_2295559 320.7768556
ILMN_1735045 131.3713396
ILMN_1680754 147.6301566

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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