Return to search results Title: RNA-Seq of Xenopus tail regeneration

Summary

In contrast to humans, many amphibians are able to rapidly and completely regenerate complex tissues, including complete appendages. Following tail amputation, Xenopus tropicalis tadpoles quickly regenerate muscle, spinal cord, cartilage, vasculature and skin, all properly patterned in three dimensions. To better understand the molecular basis of this regenerative competence, we performed a transcriptional analysis of regeneration using RNA-Seq. We profiled the transcriptome at 6 timepoints during tail regeneration, and used clustering analysis to identify biological processes that are prioritized during different transitions in the regeneration process. Our work expands significantly on previous expression analyses of tail regeneration. We are able to refine the windows during which many key biological signaling processes act, including embryonic patterning signals, immune responses, bioelectrical signaling and apoptosis. By including multiple timepoints within the first 24 hours post-amputation, we have also identified new processes that are highly prioritized early in regeneration, including axonogenesis, chemotaxis, and RNA metabolism. Our work provides a deep database for researchers interested in appendage regeneration, and highlights new avenues for further study.

Contributors: Jessica Chang, Jessica Chang, Andrea Wills, Julie Baker

Experiment Type: Whole tail (WT) samples were obtained from an an initial amputation. Immediately thereafter, a second amputation was performed on the cut tadpole to obtain 0 hour time point samples. The 0 hpa time point samples the tissue directly adjacent to the initial cut site. Regenerating tail samples collected up to 72 hpa. Expression profiling of six time points in tadpole tail regeneration were sequenced in duplicate via Illumina HiSeq.


Article: XB-ART-53040, PubMed

Source: NCBI GEO, Xenbase Download

Sample	View		GSMs	Assay Type
tail - NF40 GSM2356631  GSM2356632  RNA-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody tail NF stage 40      regenerating tail + tail amputation - NF40 DEG GSM2356633  GSM2356634  RNA-Seq Xtr   [-] [+] Background: Xtr.Outbred Manipulations: Manipulation Type Reagent Target Gene Stage Treatment Area amputation/regeneration   NF stage 40 tail Conditions: Tissue Assay Stages ChIP Antibody regenerating tail NF stage 40   regenerating tail + tail amputation - NF40 +6h GSM2356635  RNA-Seq Xtr   [-] [+] Background: Xtr.Outbred Manipulations: Manipulation Type Reagent Target Gene Stage Treatment Area amputation/regeneration   NF stage 40 tail Conditions: Tissue Assay Stages ChIP Antibody regenerating tail NF stage 40   regenerating tail + tail amputation - NF42 +15hpa GSM2356636  RNA-Seq Xtr   [-] [+] Background: Xtr.Outbred Manipulations: Manipulation Type Reagent Target Gene Stage Treatment Area amputation/regeneration   NF stage 40 tail Conditions: Tissue Assay Stages ChIP Antibody regenerating tail NF stage 42   regenerating tail + tail amputation - NF43 +24hpa GSM2356637  GSM2356638  RNA-Seq Xtr   [-] [+] Background: Xtr.Outbred Manipulations: Manipulation Type Reagent Target Gene Stage Treatment Area amputation/regeneration   NF stage 40 tail Conditions: Tissue Assay Stages ChIP Antibody regenerating tail NF stage 43   regenerating tail + tail amputation - NF47 +72hpa GSM2356639  GSM2356640  RNA-Seq Xtr   [-] [+] Background: Xtr.Outbred Manipulations: Manipulation Type Reagent Target Gene Stage Treatment Area amputation/regeneration   NF stage 40 tail Conditions: Tissue Assay Stages ChIP Antibody regenerating tail NF stage 47

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