|
| Status |
Public on Jan 31, 2019 |
| Title |
CONTROL 6hr replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
1.0mm distal tip of amputated, regenerating axolotl embryo tails, at 6 hpa. Samples were untreated.
|
| Organism |
Ambystoma mexicanum |
| Characteristics |
time (hpa): 6
treatment: Control
|
| Treatment protocol |
Developmental stage 42 (Bordzilovskaya et al 1989) axolotl embryos were manually hatched by removing the egg jelly and membrane, anesthetized in 0.02% benzocaine, and administered tail amputations with a razor blade to remove 2 mm (~20% of the body length) of the distal tail tip. After amputation, animals were placed into microtiter plates containing rearing water (40% modified Holtfreter’s Solution) and 0.001% DMSO (controls) or rearing water with 10 um romidepsin or 10 um belinostat (treatements).
|
| Growth protocol |
The use of pre-feeding stage axolotls does not require a protocol approved by the Institutional Animal Care and Use Committee (IACUC) at University of Kentucky, however embryos used in this study were treated according to the same ethical standards that apply to feeding axolotls. Rearing water (40% modified Holtfretter's solution) was changed three times per week.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The tissue samples were maintained at 4 C in RNA later prior to RNA isolation using first the Trizol method and then a Qiagen minikit with on-the-column DNAse treatment of DNA.
|
| Label |
biotin
|
| Label protocol |
Biotinylation was carried out according to the instructions in Affymetrix's 3'IVT Reagent Kit user's manual
|
| |
|
| Hybridization protocol |
Microarray hybridization using an Ambystoma Affymetrix array (Huggins et al., 2012) was performed by the University of Kentucky Microarray Core Facility.
|
| Scan protocol |
Affymetrix Command Console was used according to manufacturer's instructions
|
| Description |
RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, regenerating axolotl embryo tail tip tissue. Samples were untreated and collected 6 hours post amputation.
|
| Data processing |
GeneChips were normalized using the affy R package (Gautier et al 2004) Affymetrix Expression Console software to accomplish robust multichip averaging (RMA) (Irizarry et al., 2003).
|
| |
|
| Submission date |
Aug 14, 2018 |
| Last update date |
Jan 31, 2019 |
| Contact name |
Varun Bhamidipati Dwaraka |
| E-mail(s) |
varun.dwaraka@uky.edu
|
| Organization name |
University of Kentucky
|
| Department |
Spinal Cord and Brain Injury Research Center
|
| Lab |
Voss Lab
|
| Street address |
741 South Limestone St.
|
| City |
Lexington |
| State/province |
Kentucky |
| ZIP/Postal code |
40536-0509 |
| Country |
USA |
| |
|
| Platform ID |
GPL25286 |
| Series (1) |
| GSE118515 |
HDAC Regulates Transcription at the Outset of Axolotl Tail Regeneration |
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