|
| Status |
Public on Jun 15, 2006 |
| Title |
UD rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
SH-SY5Y neuronal cells
|
| Organism |
Homo sapiens |
| Characteristics |
SH-SY5Y neuroblastoma cells obtained from ATCC.
UD -Undifferentiated cells (before PMA addition).
|
| Treatment protocol |
SH-SY5Y human neuroblastoma cells (ATCC) were grown in complete minimal essential media (MEM) with 15% fetal calf serum in a large tissue culture flasks until 70-80% confluency. Differentiation was induced by adding 16 nM PMA resulting in neuronal phenotype. 12 h prior to PMA addition, transfect the cells with methylated oligonucleotide MeCP2 decoy (MD),which blocks the the binding of MeCP2 to the endogenous sites. Transfection with control decoy is also performed (CD).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriZol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 1 microgram of biotinylated cRNA were hybridized on GeneChip Human HG U133 plus 2.0 array for 16 hr at 45C in a GeneChip hybridization oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix 3000 GeneChip scanner.
|
| Description |
Gene expression data from experimental treatment UD = Undifferentiated SH-SY5Y cells, i.e. before PMA induced differentiation (UD).
|
| Data processing |
The data were analyzed with dChip analysis software available at http://biosun1.harvard.edu/complab/dchip/. With Invariant set normalization and Model based expression analysis.
|
| |
|
| Submission date |
Apr 03, 2006 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Sailaja Peddada |
| Organization name |
University of California, Davis
|
| Department |
Medical Microbiology and Immunology
|
| Lab |
LaSalle Lab
|
| Street address |
3426 Tupper Hall, One Shields Avenue
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE4600 |
Identifying targets of MeCP2 during neuronal maturational differentiation |
|
| Relations |
| Reanalyzed by |
GSE64985 |
| Reanalyzed by |
GSE119087 |
