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Sample GSM1130225 Query DataSets for GSM1130225
Status Public on Jan 31, 2014
Title bkg_067 [liver from HCC patient]
Sample type RNA
 
Source name bkg_067
Organism Homo sapiens
Characteristics disease state: hepatocellular carcinoma
tissue: AS-FFPE liver (cirrhotic)
%p-call: 0.403271136656594
inter-sample correlation: 0.796258964438102
prediction in as-ffpe: good
prediction confidence p-value in as-ffpe: 0.181409295
prediction in as-ffpe (%p-call >20%): good
prediction confidence p-value in as-ffpe (%p-call >20%): 0.207396302
prediction in fc-ffpe: good
prediction confidence p-value in fc-ffpe: 0.312343828
geo accession of fc-ffpe profile: GSM256386
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: bkg_067
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 GSM256386

Data table header descriptions
ID_REF
VALUE Normalized signal intensities

Data table
ID_REF VALUE
ILMN_1762337 43.39208502
ILMN_2055271 187.7654116
ILMN_1736007 50.42037569
ILMN_2383229 1624.381926
ILMN_1806310 1366.251151
ILMN_1779670 378.9124424
ILMN_1653355 63.63310491
ILMN_1717783 124.2885942
ILMN_1705025 51.27539028
ILMN_1814316 1001.955317
ILMN_2359168 1215.136719
ILMN_1731507 38.27146796
ILMN_1787689 123.3556257
ILMN_3241953 257.6021232
ILMN_1745607 18916.4556
ILMN_2136495 54.10303125
ILMN_1668111 42.50140805
ILMN_2295559 287.9468131
ILMN_1735045 187.2514039
ILMN_1680754 101.1387252

Total number of rows: 47323

Table truncated, full table size 1149 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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