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Sample GSM662425 Query DataSets for GSM662425
Status Public on Dec 31, 2016
Title Gastric tumor tissue KG061C
Sample type RNA
 
Source name Gastric tumor tissue
Organism Homo sapiens
Characteristics adjuvant chemotherapy (1=yes, 0=no, na=not available): 1
patient: KG061C
tumor type: GC
gender: M
age: 66
location: Antrum
lauren classification: Diffuse
ajcc stage: 4
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 5.62
ILMN_2055271 6.493
ILMN_1736007 5.783
ILMN_2383229 8.366
ILMN_1806310 9.358
ILMN_1779670 5.703
ILMN_2321282 6.112
ILMN_1671474 5.736
ILMN_1772582 5.876
ILMN_1735698 5.861
ILMN_1653355 6.363
ILMN_1717783 5.797
ILMN_1705025 6.19
ILMN_1814316 5.603
ILMN_2359168 5.713
ILMN_1731507 5.834
ILMN_1787689 5.889
ILMN_1745607 12.179
ILMN_2136495 5.61
ILMN_1668111 5.794

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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