GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE34394 Query DataSets for GSE34394
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
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.
Overall design The experiment includes two time course data sets. One is from mouse digit amputation, another is from Axolotl digit amputation
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
Street address 200 First St. SW
City Rochester
State/province MN
ZIP/Postal code 55905
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL14997 Illumina Genome Analyzer IIx (Ambystoma mexicanum)
Samples (20)
GSM848190 Mouse digit 0hr
GSM848191 Mouse digit 3hr
GSM848192 Mouse digit 6hr
SRA SRP009800
BioProject PRJNA149573

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE34394_RAW.tar 6.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap