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| Status |
Public on Jan 30, 2017 |
| Title |
RNA-Seq of Xenopus tail regeneration |
| Organism |
Xenopus tropicalis |
| Experiment type |
Expression profiling by high throughput sequencing
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| 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.
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| Overall design |
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.
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| Contributor(s) |
Chang JK, Wills AE, Baker JC |
| Citation(s) |
28095651 |
| Submission date |
Oct 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jessica Kay Chang |
| Organization name |
Stanford University
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| Department |
Genetics
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| Lab |
Baker
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| Street address |
300 Pasteur Drive, Alway Building M311
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL21874 |
Illumina HiSeq 2000 (Xenopus tropicalis) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA349464 |
| SRA |
SRP091865 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE88975_Tadpole.Tail.Regeneration_Count.Data.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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