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| Status |
Public on Sep 01, 2016 |
| Title |
RNA Seq analysis of gene expression in Planaria at 24, 48, 72, and 96 hours after exposure to 6k rad of gamma irradiation. |
| Organism |
Schmidtea mediterranea |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Epidermis is essential for animal survival, providing both a protective barrier and cellular sensor to the external environment. Interestingly, the epidermes of different species show broad morphological and functional diversity yet it is unclear whether this diversity came from modification of an existing gene regulatory network or de novo innovation of new genes. Here we identify the transcriptional regulators underlying the differentiation program of planarian epidermal lineage. We classify Smed-p53 as the most upstream molecule in this transcriptional cascade, suggesting a potentially conserved role for this gene in epidermal differentiation similar to TP63 in vertebrates. Moreover, we find that homologs of Sox and Pax family transcription factors, Smed-soxP-3 and Smed-pax-5, act cooperatively to activate the expression of epidermal markers. Together, these data show that planarian epidermal differentiation is regulated by a combination of conserved elements (p53/p63), recruitment of a non-conventional transcription module (soxP-3/pax-5), and novel genes (prog); they also suggest that specialized adpatations, such as epidermal mucus-secretion, arise from complex changes to gene networks. The purpose of this experiment is to identify genes associated with neoblasts (stem cells). Worms are exposed to 6k rad of gamma radiation, allowed to recover for 24, 48, 72, or 96 hours, and compared to the pre-cursor un-exposed population by RNA Seq to identify genes with decreased expression following radiation exposure.
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| Overall design |
Examine gene expression in adult flatworms at 0, 24, 48, 72, or 96 hours after exposure to 6k rad of gamma irradiation. The experiment was performed in triplicate resulting in 15 samples.
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| Contributor(s) |
Cheng L, Seidel CW, Alvarado AS |
| Citation missing |
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| Submission date |
Apr 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Chris W Seidel |
| E-mail(s) |
seidel@phageT4.org
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| Phone |
816 926 9054
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| Organization name |
Stowers Institute
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| Department |
Genomics
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| Lab |
Seidel
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| Street address |
1000 E 50th St
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| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
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| Platforms (1) |
| GPL15553 |
Illumina HiSeq 2000 (Schmidtea mediterranea) |
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| Samples (15)
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| This SubSeries is part of SuperSeries: |
| GSE80562 |
The cell type and dynamic complexity of the planarian epidermis is determined by both conserved and derived transcriptional regulators. |
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| Relations |
| BioProject |
PRJNA319241 |
| SRA |
SRP073670 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE80540_rpkm.txt.gz |
3.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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