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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 01, 2013 |
| Title |
Three Distinct Phases of Regeneration-Specific Gene Expression in the Axolotl Blastema |
| Organisms |
Ambystoma mexicanum; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The salamander has the remarkable ability to regenerate its limb after amputation. Cells at the site of amputation form a blastema and then proliferate and differentiate to regrow the limb. To better understand this process, we have performed deep RNA sequencing of the blastema over a time course. We find genes expressed in three phases with a prominent burst in oncogene expression during the first day, blastemal/limb bud genes peaking at 7 to 14 days, and markers for terminal differentiation upregulated later. We compare these expression patterns to those in a mouse digit amputation model to identify genes specific to the regenerative response. We find that limb patterning genes, SALL genes, and genes involved in the proteasome, adult stem cell, embryonic stem cell, retinoid metabolism, and WNT and NOTCH signaling are regeneration-specific. We establish the “Axolomics” Database, which provides a tool for depositing, retrieving, and searching axolotl-related “omic” information.
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| Overall design |
The experiment includes two time course data sets. One is from mouse digit amputation, another is from Axolotl digit amputation
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| Contributor(s) |
Stewart R, Rascón CA, Tian S, Nie J, Probasco MD, Bolin JM, Sengupta VA, Volkmer M, Habermann B, Badylak S, Tanaka EM, Thomson JA, Dewey CN |
| Citation(s) |
23505351 |
| Submission date |
Dec 12, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeff Nie |
| Organization name |
Mayo Clinic
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| Street address |
200 First St. SW
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| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
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| Platforms (2) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL14997 |
Illumina Genome Analyzer IIx (Ambystoma mexicanum) |
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| Samples (20)
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| Relations |
| SRA |
SRP009800 |
| BioProject |
PRJNA149573 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE34394_RAW.tar |
6.9 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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