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Series GSE4738 Query DataSets for GSE4738
Status Public on Aug 11, 2006
Title Global analysis of gene expression in Xenopus hindlimbs during stage-dependent complete and incomplete regeneration
Organism Xenopus laevis
Experiment type Expression profiling by array
Summary Xenopus laevis tadpoles are capable of limb regeneration following amputation, in a process which initially involves the formation of a blastema. However, Xenopus has full regenerative capacity only through premetamorphic stages. We have used the Affymetrix Xenopus laevis Genome Genechip® microarray to perform a large-scale screen of gene expression in the regeneration-complete, stage 53 (st53), and regeneration-incomplete, stage 57 (st57), hindlimbs at 1 and 5 days post-amputation. Through an exhaustive reannotation of the Genechip® and a variety of comparative bioinformatic analyses, we have identified genes that are differentially expressed between the regeneration-complete and –incomplete stages, detected the transcriptional changes associated with the regenerating blastema, and compared these results with those of other regeneration researchers. We focus particular attention on striking transcriptional activity observed in genes associated with patterning, stress response, and inflammation. Overall, this work provides the most comprehensive views yet of a regenerating limb and different transcriptional compositions of regeneration-competent and deficient tissues.
Keywords: Expression profiling
Overall design This experiment measures gene expression in regeneration competent stage 53 and regeneration non-competent stage 57 Xenopus laevis hindlimbs, at 1 and 5 days post-amputation. Four replicates for each condition were used. Hindlimbs at either st53 or st57 were amputated unilaterally or bilaterally at the mid-zeugopodia level. One (1dPA) and 5 days (5dPA) after amputation tissues were collected 1mm proximal to the original level of amputation. Total RNA was isolated using RNaqueous micro kit (Ambion, inc.). One microgram of total RNA was amplified with the the Affymetrix 2 cycle kit and assayed per Genechip using standard Affymetrix protocols.
Contributor(s) Grow MW, Neff AW, Mescher AL, King MW
Citation(s) 16871633
Submission date Apr 28, 2006
Last update date Mar 16, 2012
Contact name Matthew Grow
Organization name Indiana University
Department Biochemistry and Molecular Biology
Lab Center for Medical Genomics
Street address 1345 W 16th St
City Indianapolis
State/province IN
ZIP/Postal code 46202
Country USA
Platforms (1)
GPL1318 [Xenopus_laevis] Affymetrix Xenopus laevis Genome Array
Samples (16)
GSM107056 53_1dPA_MK02X001
GSM107057 53_1dPA_MK02X002
GSM107058 53_1dPA_MK02X003
BioProject PRJNA95677

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