|
| Status |
Public on Dec 12, 2012 |
| Title |
Otic Ectoderm rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
Stage 10 Chick Otic ectoderm, freshly dissected
|
| Organism |
Gallus gallus |
| Characteristics |
condition: Otic Ectoderm
|
| Treatment protocol |
Samples 5-8 were grown in defined medium +/- FGF2. Samples 1-4 were freshly dissected from chick embryos
|
| Growth protocol |
Samples 5 and 6 were grown in DMEM/F12 + N2 supplements. Samples 7 and 8 were grown in the same conditions + 50ng/ml FGF2. Samples 5-8 were cultured in collagen gels for 18 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells lysis was performed using QIAshredder columns (Qiagen) and RNA isolated using the RNeasy Micro kits (Qiagen) according to the manufacturer’s protocols, although the DNAseI step was omitted and an additional RNA cleanup step was employed.
|
| Label |
Biotin
|
| Label protocol |
RNA was amplified and biotinylated using the Two-Cycle cDNA synthesis kit and IVT labeling kit (Affymetrix)
|
| |
|
| Hybridization protocol |
standard Affymetrix protocol
|
| Scan protocol |
standard Affymetrix protocol
|
| Data processing |
Differential gene expression was analyzed using Bioconductor’s Limma package (www.bioconductor.org) and probes ranked by fold up-regulation using Excel. A cut off value of 2-fold up-regulation was selected to generate the otic and FGF-specific gene sets.
|
| |
|
| Submission date |
Dec 11, 2012 |
| Last update date |
Dec 12, 2012 |
| Contact name |
Andrew Groves |
| E-mail(s) |
akgroves@bcm.edu
|
| Phone |
7137988743
|
| Organization name |
Baylor College of Medicine
|
| Department |
Molecular and Human Genetics
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL3213 |
| Series (1) |
| GSE42845 |
Chick Otic Placode Induction Arrays |
|
