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Sample GSM257347 Query DataSets for GSM257347
Status Public on Sep 08, 2009
Title Hepatocellular carcinoma (hcc_093)
Sample type RNA
 
Source name hepatocellular carcinoma
Organism Homo sapiens
Characteristics hepatitis b virus (hbs antigen): positive
hepatitis c virus: negative
alcohol (cumulative intake): <100kg
Extracted molecule total RNA
Extraction protocol Using 10µm sections taken from formalin-fixed paraffin-embeded tissue blocks, total RNA was extracted using High Pure Paraffin FFPE kit (Roche).
Label Cy3 and Cy5
Label protocol Refer to the Illumina DASL Assay System Manual
 
Hybridization protocol Refer to the Illumina DASL Assay System Manual. Hybridization was performed for 4 DASL assay oligo pool (DAP)s, DAP1~4, including 1536 probes each on 4 separate microarrays.
Scan protocol Refer to the Illumina DASL Assay System Manual
Description na
Surgically resected 118 tumor tissues from patients with hepatocellular carcinoma (HCC)
Data processing For each probe, Red and Green intensities are computed as average of single bead values. The final signal is the sum of the Red and Green intensities. Data were were then normalized using the cubic spline algorithm for each DAP.
 
Submission date Jan 16, 2008
Last update date Jul 29, 2014
Contact name Yujin Hoshida
E-mail(s) Yujin.Hoshida@UTSouthwestern.edu
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 GPL5474
Series (1)
GSE10186 Integrative Transcriptome Analysis Reveals Common Molecular Subtypes of Human Hepatocellular Carcinoma
Relations
Affiliated with GSM1130304

Data table header descriptions
ID_REF
VALUE Normalized signal intensities by GenePattern Illumina module

Data table
ID_REF VALUE
DAP1_0003 15198.09107
DAP1_0010 13429.08266
DAP1_0021 1481.754317
DAP1_0023 1473.054213
DAP1_0027 6883.493734
DAP1_0028 634.5529338
DAP1_0030 5005.026887
DAP1_0031 11611.12772
DAP1_0033 5943.870034
DAP1_0036 2882.785004
DAP1_0038 2286.526597
DAP1_0040 25875.88366
DAP1_0041 914.987486
DAP1_0042 1160.223498
DAP1_0050 10761.59823
DAP1_0051 645.1505155
DAP1_0054 12509.78347
DAP1_0056 18449.78633
DAP1_0061 6211.49682
DAP1_0062 1368.041623

Total number of rows: 6144

Table truncated, full table size 131 Kbytes.




Supplementary file Size Download File type/resource
GSM257347_1478217_R006_C002.txt.gz 244.1 Kb (ftp)(http) TXT
GSM257347_1478233_R006_C002.txt.gz 259.1 Kb (ftp)(http) TXT
GSM257347_1478250_R006_C002.txt.gz 247.3 Kb (ftp)(http) TXT
GSM257347_1478268_R006_C002.txt.gz 262.2 Kb (ftp)(http) TXT
Processed data included within Sample table

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