|
| Status |
Public on Dec 15, 2012 |
| Title |
NEB_RA-Ag1.3_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Neuralized embryoid bodies, all trans retinoic acid (500nM) and Smo agonist (Ag1.3), 3 days
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Gli1-FLAG ESC-derived neural progenitors
treatment: all trans retinoic acid (500nM) and Smo agonist (Ag1.3, 50nM)
|
| Treatment protocol |
Cells were treated for 3 days with all trans retinoic acid (500nM) or all trans retinoic acid (500nM) and Smo agonist (Ag1.3, 50nM).
|
| Growth protocol |
Embryoid bodies were formed by culturing Rosa26-Gli1-FLAG ESCs in low attachment plates in suspension in DFNK medium. After two days of the suspension culture, cells were treated with differentiation inducers (see below) for 3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with mirVana kit from Ambion
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard protocol (3' IVT express kit, Affymetrix, P/N 901228) from 2.5ug total RNA
|
| |
|
| Hybridization protocol |
13.5 mg of fragmented biotinylated cRNA was fragmented and hybridized for 16 hr at 45C on Mouse Genome 430 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
Arrays were scanned with the GeneChip Scanner 3000 7G.
|
| Description |
Neural progenitors were formed by suspension culture in differentiation medium (DFNB) of an ESC line constitutively expressing Gli1-FLAG transgene from Rosa26 promoter. Two days into the suspension culture, cells were induced with 500nM of all-trans retinoic acid and 50nM of Smo agonist (Ag1.3) for additional 3 days before harvested for total RNA extraction.
|
| Data processing |
Data were analyzed with dChip
|
| |
|
| Submission date |
Nov 27, 2012 |
| Last update date |
Dec 15, 2012 |
| Contact name |
Kevin Peterson |
| E-mail(s) |
kevin.peterson@med.usc.edu
|
| Phone |
323-442-8077
|
| Organization name |
Eli and Edythe Broad-CIRM Center for Regenerative Medicine, University of Southern California Keck School of Medicine
|
| Department |
Department of Stem Cell Biology and Regenerative Medicine
|
| Lab |
Andrew McMahon
|
| Street address |
1425 San Pablo St.
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE42565 |
Transcriptional responses to Sonic Hedgehog pathway stimulation in in vitro derived neural progenitors |
| GSE42594 |
cis-Regulation of Shh-directed neural pattering |
|
