|
| Status |
Public on Feb 28, 2014 |
| Title |
Tris and Retinoic Acid biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Stage 18 chicken embryos
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: Mesenchyme plus epithelium, maxillary
treatment: Tris and Retinoic Acid
age: Hamburger Hamilton stage 18
|
| Treatment protocol |
Four different treatments were done each consisting of two beads placed into the side of the head between the eye and mandibular arch. Beads were soaked in 1 mg/ml Noggin protein (Affigel blue beads, 200 microns in diameter) or 1 mg/ml all-trans-retinoic acid (AG1X2, Formate form, 100 microns) for a minimum of 1 hour prior to implantation. Control beads were soaked in Tris (buffer for Noggin) or dimethylsulfoxide (solvent for retinoic acid). The following combinations were implanted, Noggin+ RA, Tris+RA, Noggin+DMSO, Tris+DMSO. All animals had bead implants.
|
| Growth protocol |
Embryos were incubated at 38 degrees C until they reached Hamburger Hamilton Stage 15 or 25 somites. Beads were implanted and then embryos were reincubated for another 16h until they reached stage 18. Maxillary tissues were dissected from 12-15 embryos and pooled together to form one biological replicate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNAeasy kit was used.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to two-cycle Affymetrix protocol from 500 ng total RNA (GeneChip Expression Analysis Technical Manual, Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridization was performed as described in the GeneChip Expression Analysis Technical Manual by the London Regional Genomics Centre, London, Ontario, Canada
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip scanner 3000
|
| Description |
Gene expression data from stage 18 maxillary prominences, 16h post treatment
|
| Data processing |
The data were analyzed with GCOS1.4 using Affymetrix default analysis settings and Scaling within 3 fold of each other as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
|
| |
|
| Submission date |
Nov 08, 2013 |
| Last update date |
Feb 28, 2014 |
| Contact name |
Joy Richman |
| E-mail(s) |
[email protected]
|
| Organization name |
University of British Columbia
|
| Department |
Oral Health Sciences
|
| Street address |
2350 Health Sciences Mall
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6T 1Z3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL3213 |
| Series (1) |
| GSE52227 |
Discovery of genes involved in facial midline specification |
|
