|
| Status |
Public on Jun 05, 2015 |
| Title |
SH-SY5Y cells with Control shRNA replicate1 |
| Sample type |
RNA |
| |
|
| Source name |
Human SH-SY5Y cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SH-SY5Y
transfection: control shRNA
|
| Treatment protocol |
SH-SY5Y cells were seeded onto collagen-coated plates at an initial density of 104 cells/cm2. Retinoic acid (RA) (Sigma) was added at a final concentration of 10 μM the next day after plating. After 4 days, the cells were washed three times with PBS and incubated with 50 ng/mL of Brain Derived Neural Factor (BDNF) (Millipore) in serum-free medium for 3 days.
|
| Growth protocol |
SH-SY5Y were maintained in Dulbecco's Modified Eagle Medium (DMEM) containing 4,500 mg/L glucose, 10% heat-inactivated fetal bovine serum, 110 mg/L sodium pyruvate, 2 mM L-glutamine and 1% penicillin-streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells at indicated time point with RNeasy Mini Kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit. WT Expression Kit
|
| |
|
| Hybridization protocol |
Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scaned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.
|
| Description |
SH-SY5Y cells were induced differentiation with Brain Derived Neural Factor (BDNF) for 3 days
|
| Data processing |
The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.
|
| |
|
| Submission date |
Nov 07, 2014 |
| Last update date |
Jun 05, 2015 |
| Contact name |
Ruitu Lyu |
| E-mail(s) |
lvruitu@gmail.com
|
| Organization name |
Institutes of Biomedical Sciences Fudan University
|
| Lab |
Epigenetics lab
|
| Street address |
138 Yixueyuan Road Xuhui District
|
| City |
Shanghai |
| ZIP/Postal code |
200030 |
| Country |
China |
| |
|
| Platform ID |
GPL17586 |
| Series (2) |
| GSE63097 |
The LSD1/KDM1A neuro-specific isoform regulates neuronal differentiation through H3K9 demethylation [Affymetrix] |
| GSE63153 |
The LSD1/KDM1A neuro-specific isoform regulates neuronal differentiation through H3K9 demethylation |
|
