|
| Status |
Public on Sep 01, 2009 |
| Title |
SH-SY5Y(ATCC)_RA_3d_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
neuroblastoma cell, retinoic acid (RA), 3day
|
| Organism |
Homo sapiens |
| Characteristics |
Cell line: SH-SY5Y (CRL-2266, obtained from ATCC (American Type Culture Collection Cultures))
|
| Treatment protocol |
SH-SY5Y-A cells were seeded in laminin coated culture dishes (BioCoat Laminin Cellware; BD Biosciences) for 1 day and then transferred to a medium containing 10 μM of RA for five days.
|
| Growth protocol |
Tissue culture cells were maintained in D-MEM/F12 1:1 mixture supplemented with 15% FBS (Fetal Bovine Serum) and 1% NEAA (Non-essential amino acid) in a 5% CO2 humidified incubator at 37oC. The culture medium was changed twice a week.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was extracted from the cells at specific intervals using the RiboPure Kit (Ambion, An Applied Biosystems Business, Austin, TX, USA) according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
First-strand cDNA was synthesized using 5 μg of total RNA and the GeneChip One-cycle cDNA Synthesis Kit (Affymetrix, Inc.). Biotin-labeled cRNA was generated by the GeneChip IVT labeling Kit (Affymetrix, Inc.)
|
| |
|
| Hybridization protocol |
Biotin-labeled cRNA was applied on the Human Genome U133 Plus 2.0 Array (Affymetrix, Inc.) and then hybridized at 45oC for 17 h in a GeneChip Hybridization Oven (Affymetrix, Inc.).
|
| Scan protocol |
Washing, staining and scanning of the array were performed using the GeneChip Wash and Stain Kit and a GeneChip Scanner 3000 (Affymetrix, Inc.), respectively.
|
| Description |
Sampling of RNA was performed at six different time points (0h, 6h, 1d, 2d, 3d, and 5d, respectively) under RA inducible conditions.
|
| Data processing |
The average signal intensity for all probes was initially tuned to 500 as global scaling and individual signal intensities were evaluated by detection call (present/marginal/absent) using the Affymetrix Micro Array Suite 5.0 (MAS 5.0) software (Affymetrix, Inc.).
|
| |
|
| Submission date |
Sep 26, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Tadayuki Takeda |
| E-mail(s) |
[email protected]
|
| Phone |
(+81) 45 503 9286
|
| Fax |
(+81) 45 503 9176
|
| URL |
http://hgp.gsc.riken.go.jp/index.php/Main_Page
|
| Organization name |
RIKEN GSC
|
| Department |
Computatinal and Experimental Systems Biology Group
|
| Lab |
Genome Annotation and Comparative Analysis Team
|
| Street address |
1-7-22, Suehiro-cho, Tsurumi-ku
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE9169 |
Gene expression during neuronal differentiation in two subtypes of SH-SY5Y |
|
