|
| Status |
Public on Apr 30, 2012 |
| Title |
MDA003 |
| Sample type |
RNA |
| |
|
| Source name |
gastric tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
sample_id: MDA003
gender: Male
baseline stage: IV
grade: G3
|
| 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-6 V2.0 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 48701 probes on the Human-6 beadChip ver. 2 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, Sample Gene Profile option of this software was used.
|
| |
|
| Submission date |
Apr 12, 2011 |
| Last update date |
Apr 30, 2012 |
| 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 |
GPL13376 |
| Series (1) |
| GSE28541 |
Characterization of gene expression profiles of gastric cancer in MD Anderson Cancer Center cohort |
|
