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Sample GSM256480 Query DataSets for GSM256480
Status Public on Oct 15, 2008
Title Hepatocellular carcinoma (hcc_078)
Sample type RNA
 
Source name hepatocellular carcinoma
Organism Homo sapiens
Characteristics used for prognostic prediction: No
survival time (days): 2832
survival status (0: alive or censored, 1: dead) : 0
hepatitis b virus (hbs antigen): negative
hepatitis c virus: negative
alcohol (cumulative intake): >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
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
Relations
Affiliated with GSM1130294

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

Data table
ID_REF VALUE
DAP1_0003 9931.927243
DAP1_0010 10732.61117
DAP1_0021 3483.822229
DAP1_0023 1254.268051
DAP1_0027 2372.117882
DAP1_0028 722.0326135
DAP1_0030 10137.87474
DAP1_0031 8509.365324
DAP1_0033 976.9789916
DAP1_0036 1494.47758
DAP1_0038 8509.365324
DAP1_0040 13676.19446
DAP1_0041 1321.063354
DAP1_0042 5817.281241
DAP1_0050 9276.320687
DAP1_0051 5354.0635
DAP1_0054 6652.661957
DAP1_0056 12041.5974
DAP1_0061 1321.063354
DAP1_0062 3197.784943

Total number of rows: 6144

Table truncated, full table size 131 Kbytes.




Supplementary file Size Download File type/resource
GSM256480_1478276_R007_C010.txt.gz 248.1 Kb (ftp)(http) TXT
GSM256480_1478292_R007_C010.txt.gz 260.2 Kb (ftp)(http) TXT
GSM256480_1478305_R007_C010.txt.gz 258.7 Kb (ftp)(http) TXT
GSM256480_1478313_R007_C010.txt.gz 253.9 Kb (ftp)(http) TXT
Processed data included within Sample table

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