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Sample GSM256493 Query DataSets for GSM256493
Status Public on Oct 15, 2008
Title Hepatocellular carcinoma (hcc_106)
Sample type RNA
 
Source name hepatocellular carcinoma
Organism Homo sapiens
Characteristics used for prognostic prediction: Yes
survival time (days): 913
survival status (0: alive or censored, 1: dead) : 1
hepatitis b virus (hbs antigen): negative
hepatitis c virus: positive
alcohol (cumulative intake): none
microvascular invasion: negative
satellite lesions: negative
Treatment protocol na
Growth protocol na
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 none
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 10, 2008
Last update date Dec 15, 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 (4)
GSE10141 Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma (Training Set, HCC)
GSE10143 Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma
GSE10186 Integrative Transcriptome Analysis Reveals Common Molecular Subtypes of Human Hepatocellular Carcinoma

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

Data table
ID_REF VALUE
DAP1_0003 4244.415642
DAP1_0010 15461.87637
DAP1_0021 1943.231104
DAP1_0023 1166.440361
DAP1_0027 799.0978857
DAP1_0028 1339.261382
DAP1_0030 5355.857129
DAP1_0031 15461.87637
DAP1_0033 953.0191382
DAP1_0036 1413.302897
DAP1_0038 1758.547821
DAP1_0040 19799.16744
DAP1_0041 1155.08713
DAP1_0042 7364.647344
DAP1_0050 10190.7265
DAP1_0051 3181.686543
DAP1_0054 1814.372182
DAP1_0056 8974.064918
DAP1_0061 1585.491276
DAP1_0062 5716.750243

Total number of rows: 6144

Table truncated, full table size 131 Kbytes.




Supplementary file Size Download File type/resource
GSM256493_1478217_R007_C005.txt.gz 248.8 Kb (ftp)(http) TXT
GSM256493_1478233_R007_C005.txt.gz 260.3 Kb (ftp)(http) TXT
GSM256493_1478250_R007_C005.txt.gz 241.9 Kb (ftp)(http) TXT
GSM256493_1478268_R007_C005.txt.gz 248.0 Kb (ftp)(http) TXT
Processed data included within Sample table

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