Gene Expression

The analysis of gene expression is being studied using microarray, quantitative-pcr, RNA-seq, and nanostring. These resources include:

Comprehensive analysis of gene expression during axolotl limb regeneration.

The following database shows temporal gene expression profiles from the largest microarray experiment ever performed for limb regeneration. Ten replicate Amby002 GeneChips (Huggins et al., 2012) were used to estimate gene expression for 20 different time points during limb regeneration. Two different amputation injuries were performed: amputation through the stylopod and zeugopod of the forelimb. One millimeter of the distal-most tissue of regenerating limbs was sampled for RNA isolation and microarray analysis. Overall, the database reports 8,000,000 estimates of gene expression during the first 28 days of limb regeneration.

Search for Genes, Gene Symbol or Probe ID:


Amby001: A custom Affymetrix GeneChip© with approximately 4500 perfect and mismatch probesets. Library Files Probe Annotation File (Original) Probe Annotations (Updated)

Amby002: A custom Affymetrix GeneChip© with approximately 20,000 perfect probesets. For more information, contact your local Affymetrix representative with the array name (AMBY_002a520748F) and part number - 520748. Library Files Probe Annotation File

Transcript Assemblies:

V5 Assembly (A. mexicanum compilation of multiple transcript data)

A.AND Ref (Ambystoma Andersoni de novo from Illumina RNA-Seq data)

A.MAC Ref (Ambystoma maculatum de novo assembly from Illumina RNA-Seq data)

Instructions for performing RMA analyses in Expression console

Instructions for performing RMA analyses using Partek Genomics Suite

Recent Microarray Experiments and Data:

Page RB, Boley MA, Kump DK, Voss SR. 2013. Genomics of a metamorphic timing QTL: met1 maps to a unique genomic position and regulates morph and species-specific patterns of brain transcription. Genome Biology and Evolution, In Press. Download .CEL files

Huggins P, Johnson CK, Schoergendorfer A, Putta S, Bathke AC. Stromberg AJ, Voss SR. 2011. Identification of differentially expressed thyroid hormone responsive genes from the brain of the Mexican Axolotl (Ambystoma mexicanum). Comparative Biochemistry and Physiology, Part C. doi:10.1016/j.cbpc.2011.03.006. Download .CEL files

Page RB, Boley MA, Smith JJ, Putta S, Voss SR. 2010. Microarray analysis of a salamander hopeful monster reveals transcriptional signatures of paedomorphic brain development. BMC Evol Biol, 10:199. Download .CEL files

Monaghan JR, Epp LG, Putta S, Page RB, Walker JA, Beachy CK, Zhu W, Pao GM, Verma IM, Hunter T, Bryant SV,Gardiner DM, Harkins TT, Voss SR. 2009. Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration.BMC Biology 7:1. Download .CEL files

Cotter JD, Storfer A, Page RB, Beachy CK, Voss SR. 2008. Transcriptional response of Mexican axolotls to Ambystoma tigrinum virus (ATV) infection.,BMC Genomics 9:493 Download .CEL files

Page RB, Voss SR, Samuels AK, Smith JJ, Putta S, Beachy CK. 2008. Effect of thyroid hormone concentration on the transcriptional response underlying induced metamorphosis in the Mexican axolotl, BMC Genomics 9:78 Download .CEL files

Page RB, Monaghan JR, Samuels AK, Smith JJ, Beacy CK, Voss, SR. 2007. Microarray analysis identifies keratin loci as sensitive biomarkers for thyroid hormone disruption in the salamander Ambystoma mexicanum. Comparative Biochemistry and Physiology, Part C 145:15-27 Download .CEL files

Monaghan JR, Walker JA, Page RB, Putta S, Beachy CK, Voss SR. 2007. Early gene expression during natural spinal cord regeneration in the salamander Ambystoma mexicanum. Journal of Neurochemistry 101:27-40. Download .CEL files