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Sample GSM256430 Query DataSets for GSM256430
Status Public on Oct 15, 2008
Title Hepatocellular carcinoma (hcc_011)
Sample type RNA
 
Source name hepatocellular carcinoma
Organism Homo sapiens
Characteristics used for prognostic prediction: No
survival time (days): 1868
survival status (0: alive or censored, 1: dead) : 1
hepatitis b virus (hbs antigen): negative
hepatitis c virus: positive
alcohol (cumulative intake): 500-1,000kg
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 Jul 29, 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 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
Relations
Affiliated with GSM1130245

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

Data table
ID_REF VALUE
DAP1_0003 8813.693461
DAP1_0010 14063.17798
DAP1_0021 1135.033792
DAP1_0023 1100.144369
DAP1_0027 7673.846717
DAP1_0028 668.7027035
DAP1_0030 7236.560465
DAP1_0031 13472.94331
DAP1_0033 795.5877443
DAP1_0036 3361.125694
DAP1_0038 6530.554388
DAP1_0040 25375.06859
DAP1_0041 1550.553988
DAP1_0042 2749.781601
DAP1_0050 13683.16117
DAP1_0051 4847.347962
DAP1_0054 7935.920856
DAP1_0056 20301.0032
DAP1_0061 2777.806547
DAP1_0062 13683.16117

Total number of rows: 6144

Table truncated, full table size 131 Kbytes.




Supplementary file Size Download File type/resource
GSM256430_1478321_R007_C003.txt.gz 257.4 Kb (ftp)(http) TXT
GSM256430_1478330_R007_C003.txt.gz 267.4 Kb (ftp)(http) TXT
GSM256430_1513764029.1_R007_C003.txt.gz 259.7 Kb (ftp)(http) TXT
GSM256430_1513764029.3_R007_C003.txt.gz 253.6 Kb (ftp)(http) TXT
Processed data included within Sample table

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