|
| Status |
Public on Dec 31, 2012 |
| Title |
2DG-1 |
| Sample type |
RNA |
| |
|
| Source name |
SK4 treated with 2-deoxy-glucose (4mM) for 12 hrs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SK-4
tissue type: esophageal cancer
|
| 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 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.
|
| Data processing |
Array data processing were performed on Illumina BeadStudio software. To export to a data matrix, Sample Gene Profile option of this software was used.
|
| |
|
| Submission date |
Jun 25, 2009 |
| Last update date |
Dec 31, 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 |
GPL6790 |
| Series (1) |
| GSE16816 |
Combinatorial targeting of glycolysis and oxidative phosphorylation suppresses tumor growth and metastases. |
|
