|
| Status |
Public on May 06, 2010 |
| Title |
Surrounding BS085 |
| Sample type |
RNA |
| |
|
| Source name |
Bladder mucosae surrounding cancer
|
| Organism |
Homo sapiens |
| Characteristics |
biological source: bladder mucosae surrounding cancer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from tissues with TRIzol (Life Technologies, NY) reagent according to the manufacturer’s protocol. RNA quality and integrity were confirmed by electrophoresis on agarose gel stained with ethidium bromide and examined under ultraviolet light.
|
| 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 RiboGreen were measured (Quant-iTTM RiboGreen® RNA assay kit; Invitrogen-Molecular Probes, ON, Canada) by the Victor3 spectrophotometer (PerkinElmer, CT) and cRNA quality was checked on a 1% agarose gel.
|
| |
|
| Hybridization protocol |
Labeled, amplified material (1,500 ng per array) was hybridized to a ver. 2 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 use Sample Gene Profile option of Illumina BeadStudio software. Therefore, a total of 5553 probe data which have duplicated gene aggregated unique genes from the whole 48701 probes on the Human-6 beadChip ver. 2.
|
| 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 |
Nov 07, 2008 |
| Last update date |
May 06, 2010 |
| Contact name |
Seon-Kyu Kim |
| E-mail(s) |
[email protected]
|
| Phone |
+82-42-879-8107
|
| Organization name |
Korea Research Institutue of Bioscience & Biotechnology
|
| Department |
Personalized Genomic Medicine Research Center
|
| Street address |
125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea
|
| City |
Daejeon |
| ZIP/Postal code |
305-806 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL6102 |
| Series (1) |
| GSE13507 |
Predective Value of Prognosis-Related Gene Expression Study in Primary Bladder Cancer |
|
