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Sample GSM256357 Query DataSets for GSM256357
Status Public on Oct 15, 2008
Title Hepatitis/cirrhotic liver (bkg_027)
Sample type RNA
 
Source name hepatitis/cirrhotic liver
Organism Homo sapiens
Characteristics bkg_id: bkg_027
survival time (days): 3237
survival_status (0: alive_or_censored, 1:dead): 0
ethnicity: Japanese
egf level: Low
used for prognostic prediction: Yes
recurrence status (0: no recurrence of censored, 1: recurrence): 0
time to hcc recurrence (days): 3876
early recurrence status (0: no recurrence of censored, 1: recurrence < 2 years): 0
late recurrence status (0: no recurrence of censored, 1: recurrence >= 2 years): 0
Treatment 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 (3)
GSE10140 Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma (Training Set, Liver)
GSE10143 Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma
GSE20140 Combining Clinical, Pathology, and Gene Expression Data to Predict Recurrence of Hepatocellular Carcinoma
Relations
Affiliated with GSM1130202

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

Data table
ID_REF VALUE
DAP1_0003 8377.8927142055
DAP1_0010 10934.3090818824
DAP1_0021 1135.04250331875
DAP1_0023 1255.54438026048
DAP1_0027 3786.72901983094
DAP1_0028 1010.59072293987
DAP1_0030 5171.75330353591
DAP1_0031 8164.9243541147
DAP1_0033 891.773080405855
DAP1_0036 1859.06995621032
DAP1_0038 3154.31725505619
DAP1_0040 15091.2824902101
DAP1_0041 1503.97888723799
DAP1_0042 6090.7150553477
DAP1_0050 11853.236245243
DAP1_0051 2303.1676429414
DAP1_0054 5331.15727537
DAP1_0056 19020.3715630962
DAP1_0061 2933.7246881282
DAP1_0062 745.829967788263

Total number of rows: 6144

Table truncated, full table size 161 Kbytes.




Supplementary file Size Download File type/resource
GSM256357_1478321_R006_C007.txt.gz 242.1 Kb (ftp)(http) TXT
GSM256357_1478330_R006_C007.txt.gz 237.7 Kb (ftp)(http) TXT
GSM256357_1503697.1_R006_C007.txt.gz 238.7 Kb (ftp)(http) TXT
GSM256357_1503697.3_R006_C007.txt.gz 237.9 Kb (ftp)(http) TXT
Processed data included within Sample table

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