|
| Status |
Public on Sep 17, 2012 |
| Title |
Innervated limb at D7, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Innervated limb at 7 days post injury
|
| Organism |
Ambystoma mexicanum |
| Characteristics |
tissue: Innervated limb epidermis
animal type: aquatic axolotl
time: 7 days post injury
|
| Treatment protocol |
Sterile 4mm biopsy punches were used to create flank wounds on the side of the animal. Forelimbs were amputated just proximal to the elbow and the humerus trimmed to make the amputation plane flush. Denervation was performed by transecting the brachial nerves entering the limb.
|
| Growth protocol |
Animals were housed individually at 21-23˚C in 40% Holtfreter’s Solution.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Trizol Reagent followed by Qiagen RNeasy Clean-up columns
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Affymetrix GeneChip Expression Analysis Manual)
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA were hybridized for on 32 GeneChip Axolotl Microarrays (AMBY_002a520748F) in the Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GCS 3000 7G scanner.
|
| Description |
Gene expression data from amputated innervated limb
|
| Data processing |
Microarray data was analyzed in the software system R using the Bioconductor package and oneChannelGUI. Microarray data was preprocessed and normalized using RMA and a linear model testing the effect of time for each morph type was fit for each gene across all 32 GeneChips using limma.
|
| |
|
| Submission date |
Apr 11, 2012 |
| Last update date |
Sep 18, 2012 |
| Contact name |
James R Monaghan |
| E-mail(s) |
james.monaghan@ufl.edu
|
| Phone |
352-273-7876
|
| Fax |
352-392-3993
|
| URL |
http://james-monaghan.com
|
| Organization name |
University of Florida
|
| Department |
Biology
|
| Lab |
Malcolm Maden
|
| Street address |
2033 Mowry Road
|
| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
| |
|
| Platform ID |
GPL15153 |
| Series (1) |
| GSE37198 |
Expression data from aquatic axolotl full thickness epithelial flank wounds, innervated limbs, and denervated limbs collected over seven days |
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