|
| Status |
Public on Sep 01, 2009 |
| Title |
SK-N-SH_BDNF_1d_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
neuroblastoma cell, brain-derived neurotrophic factor (BDNF), 1day
|
| Organism |
Homo sapiens |
| Characteristics |
Cell line: SH-SY5Y (HTB-11, obtained from ATCC (American Type Culture Collection Cultures))
|
| Treatment protocol |
SK-N-SH cells were washed with D-MEM/F12 twice after five days in the presence of RA and then incubated with 50 ng/ml of BDNF in D-MEM/F12 without serum for three 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 and at five different time points (0h, 6h, 1d, 2d and 3d, respectively) after the cells were transferred to serum-free medium containing BDNF.
|
| 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 |
|
