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Sample GSM348399 Query DataSets for GSM348399
Status Public on Jul 19, 2011
Title GAS_DIS_GC_YG54T_C2
Sample type RNA
 
Source name Primary gastric cancer
Organism Homo sapiens
Characteristics gastric adenocarcinoma
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer's protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)
Label Biotin
Label protocol Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina?? TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)
 
Hybridization protocol Labeled, amplified material (1,500 ng per array) was hybridized to a ver. 3 of the Illumina Human-6 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual
Scan protocol Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions
Description To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48804 probes on the Human-6 beadChip ver. 3 were used. Clinical data provided as a supplementary file on Series record: GSE13861_GE_MDACC_DepSysB_ClinicalInformation.xls.gz
Data processing Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformation. To export to a data matrix, Sample Gene Profile option of this software was used.
 
Submission date Dec 08, 2008
Last update date Jul 19, 2011
Contact name Sangbae Kim
E-mail(s) sangbkim22@gmail.com
Organization name Baylor Colleage of Medicine
Department HGSC
Street address 1 Baylor plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL6884
Series (1)
GSE13861 Gene expression signature-based novel prognostic risk score in gastric cancer

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ILMN_1809034 6.400538
ILMN_1660305 8.30337
ILMN_1792173 7.33396
ILMN_1762337 5.641835
ILMN_2055271 5.969243
ILMN_1736007 5.342341
ILMN_1814316 5.19928
ILMN_2359168 5.485105
ILMN_1731507 5.125155
ILMN_1787689 5.403609
ILMN_1745607 12.547413
ILMN_2136495 5.188243
ILMN_1668111 5.130107
ILMN_2295559 5.42156
ILMN_1735045 8.656675
ILMN_1680754 5.434628
ILMN_2375184 5.239169
ILMN_1659452 5.514438
ILMN_1767388 5.64789
ILMN_1675204 4.948601

Total number of rows: 48803

Table truncated, full table size 1045 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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