|
| Status |
Public on Jan 01, 2017 |
| Title |
SH_proliferative_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
SH-SY5Y cell line undifferentiated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SH-SY5Y
treatment: 7 days cell culture in 10% FBS medium
|
| Treatment protocol |
All-trans retinoic acid (cat. #BML-GR100/Enzo Life Science) was used in all the differentiation protocols. Purified protein BDNF (cat. #cyt-207/ProSpec-Tany TechnoGene Ltd.) was used in BDNF differentiation protocol.
|
| Growth protocol |
SH-SY5Y human neuroblastoma cells were cultured in DMEM/F12 medium (DMEM – cat. #1210-046/Life Technologies; F12 – cat. #21700-075/Life Technolgies) supplemented with 10% FBS (cat. #FB0010S/Cripion Biotecnolgia LTDA) and antibiotics. AR-only differentiation protocols were carried by decreasing FBS to 1% and adding retinoic acid (RA) 10 uM, with medium and RA maintenance at day 4. In BDNF differentiation protocol, in addition to FBS decrease and RA, BDNF 50 ng/ml was added at day 4, with medium and RA maintenance
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were isolated from cells using the extraction protocol with TRIzol Reagent (Life Technologies) with posterior purification and treatment with DNAse (Qiagen RNeasy Mini Kit and Qiagen RNase-Free DNase Set, respectively) according to manufacter's instructions.
|
| Label |
biotin
|
| Label protocol |
Samples were prepared according to standard Affymetrix protocol, from 100 ng of total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45ºC on GeneChip Human PrimeView (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).
|
| Description |
replicate 1 (batch1)
|
| Data processing |
Raw CEL files were analysed using the R/Bioconductor pipeline. The data was normalized by Robust Multi-array Average (RMA) in the AFFY package, log (base 2) transformed, and batch-corrected with ComBat in the SVA package.
|
| |
|
| Submission date |
Aug 06, 2015 |
| Last update date |
Jan 01, 2017 |
| Contact name |
Marco Antonio De Bastiani |
| E-mail(s) |
marco.bastiani@ufrgs.br
|
| Phone |
5551981468041
|
| Organization name |
Universidade Federal do Rio Grande do Sul
|
| Department |
Biochemistry
|
| Lab |
Cellular Biochemistry
|
| Street address |
Ramiro Barcelos 2600
|
| City |
Porto Alegre |
| State/province |
Rio Grande do Sul |
| ZIP/Postal code |
90035-003 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL16043 |
| Series (1) |
| GSE71817 |
Neuro-like differentiation of SH-SY5Y human cell line |
|
