title: Gene expression during the first 28 days of axolotl limb regeneration I: Experimental design and global analysis of gene expression.
abstract: While it is appreciated that global gene expression analyses can provide novel insights about complex biological processes, experiments are generally insufficiently powered to achieve this goal. Here we report the results of a robust microarray experiment of axolotl forelimb regeneration. At each of 20 post-amputation time points, we estimated gene expression for 10 replicate RNA samples that were isolated from 1 mm of heterogeneous tissue collected from the distal limb tip. We show that the limb transcription program diverges progressively with time from the non-injured state, and divergence among time adjacent samples is mostly gradual. However, punctuated episodes of transcription were identified for five intervals of time, with four of these coinciding with well-described stages of limb regeneration-amputation, early bud, late bud, and pallet. The results suggest that regeneration is highly temporally structured and regulated by mechanisms that function within narrow windows of time to coordinate transcription within and across cell types of the regenerating limb. Our results provide an integrative framework for hypothesis generation using this complex and highly informative data set.
authors.affiliation: Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA; Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky 40506, USA.
authors.forename: S Randal
authors.initials: SR
authors.lastname: Voss
authors.affiliation: Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Palumbo
authors.affiliation: Department of Biostatistics, University of Kentucky, Lexington, Kentucky 40506, USA.
authors.forename: Radha
authors.initials: R
authors.lastname: Nagarajan
authors.affiliation: Department of Developmental and Cell Biology, UC-Irvine, Irvine, California 92697, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Gardiner
authors.affiliation: Department of Molecular and Cellular Biology, Tulane University, New Orleans, Louisiana 70118, USA.
authors.forename: Ken
authors.initials: K
authors.lastname: Muneoka
authors.affiliation: Department of Statistics, University of Kentucky, Lexington, Kentucky 40506, USA.
authors.forename: Arnold J
authors.initials: AJ
authors.lastname: Stromberg
authors.affiliation: Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA; Department of Statistics, University of Kentucky, Lexington, Kentucky 40506, USA.
authors.forename: Antony T
authors.initials: AT
authors.lastname: Athippozhy
keywords: Axolotl; limb; microarray; regeneration; transcription