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Sample GSM348355 Query DataSets for GSM348355
Status Public on Jul 19, 2011
Title GAS_DIS_GC_YG07T_GIST-like_C3
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 5.700162
ILMN_1660305 7.009549
ILMN_1792173 7.505573
ILMN_1762337 5.6094
ILMN_2055271 5.595146
ILMN_1736007 5.264912
ILMN_1814316 5.227664
ILMN_2359168 5.446918
ILMN_1731507 5.172327
ILMN_1787689 5.439291
ILMN_1745607 13.231991
ILMN_2136495 5.226894
ILMN_1668111 5.260402
ILMN_2295559 5.336283
ILMN_1735045 7.407948
ILMN_1680754 5.44791
ILMN_2375184 5.304876
ILMN_1659452 5.54566
ILMN_1767388 5.28281
ILMN_1675204 5.06264

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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