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Sample GSM662436 Query DataSets for GSM662436
Status Public on Dec 31, 2016
Title Gastric tumor tissue KG072C
Sample type RNA
 
Source name Gastric tumor tissue
Organism Homo sapiens
Characteristics adjuvant chemotherapy (1=yes, 0=no, na=not available): 1
patient: KG072C
tumor type: GC
gender: M
age: 55
location: Antrum
lauren classification: Intestinal
ajcc stage: 3
tissue: Gastric tumor tissue
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer 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 (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).
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 48803 probes on the Human-12 beadChip ver. 3 were used.
Data processing Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Group Gene Profile option of this software was used.
 
Submission date Jan 27, 2011
Last update date Dec 31, 2016
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 GPL6947
Series (2)
GSE26899 Characterization of gene expression profiles of gastric cancer in the Korea University cohort
GSE26942 Characterization of gene expression profiles of gastric cancer

Data table header descriptions
ID_REF Illumina_ID
VALUE Log2 transformed normalized signal intensity.

Data table
ID_REF VALUE
ILMN_1762337 5.769
ILMN_2055271 6.122
ILMN_1736007 5.992
ILMN_2383229 7.522
ILMN_1806310 8.048
ILMN_1779670 6.027
ILMN_2321282 6.265
ILMN_1671474 5.694
ILMN_1772582 5.824
ILMN_1735698 5.786
ILMN_1653355 6.251
ILMN_1717783 5.702
ILMN_1705025 5.531
ILMN_1814316 5.828
ILMN_2359168 5.499
ILMN_1731507 5.714
ILMN_1787689 6.094
ILMN_1745607 11.49
ILMN_2136495 5.738
ILMN_1668111 5.815

Total number of rows: 48803

Table truncated, full table size 903 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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