Schmidtea mediterranea
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ABSTRACT:
PROVIDER: PRJNA320389 | ENA |
REPOSITORIES: ENA
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Project description:Proper function and repair of the digestive system are vital to most animals. Deciphering the mechanisms involved in these processes requires an atlas of gene expression and cell types. Here, we applied laser-capture microdissection (LCM) and RNA-seq to characterize the intestinal transcriptome of Schmidtea mediterranea, a planarian flatworm that can regenerate all organs, including the gut. We identified hundreds of genes with intestinal expression undetected by previous approaches. Systematic analyses revealed extensive conservation of digestive physiology and cell types with other animals, including humans. Furthermore, spatial LCM enabled us to uncover previously unappreciated regionalization of gene expression in the planarian intestine along the medio-lateral axis, especially among intestinal goblet cells. Finally, we identified two intestine-enriched transcription factors that specifically regulate regeneration (hedgehog signaling effector gli-1) or maintenance (RREB2) of goblet cells. Altogether, this work provides resources for further investigation of mechanisms involved in gastrointestinal function, repair and regeneration.
2020-03-20 | GSE135351 | GEO
Project description:Gene expression profiling of regenerating planarian tails after inhibition of myoD and follistatin
| PRJNA387024 | ENA
Project description:Hedgehog signaling is critical for vertebrate central nervous system (CNS) development, but its role in CNS biology in other organisms is poorly characterized. In the planarian Schmidtea mediterranea, hedgehog (hh) is expressed in medial cephalic ganglia neurons, suggesting a possible role in CNS maintenance or regeneration. We performed RNA sequencing of planarian brain tissue following RNAi of hh and the gene encoding its receptor, patched (ptc). We identified two misregulated genes, intermediate filament-1 (if-1) and calamari (cali), that are expressed in a previously unidentified non-neural CNS cell type. These cells expressed orthologs of astrocyte-associated genes involved in neurotransmitter uptake and metabolism, and extended processes enveloping regions of high synapse concentration. We conclude these are glia-like cells (GLCs). Planarian GLCs exist in two compartments with gene expression programs distinguished by Hh signaling. Planarian GLCs and their regulation by Hedgehog signaling present a novel tractable system for dissection of glia biology.
2016-09-28 | GSE81059 | GEO
Project description:The head-regeneration transcriptome of the planarian Schmidtea mediterranea
2011-07-15 | E-MTAB-607 | biostudies-arrayexpress
Project description:Background: Freshwater planarians are well known for their regenerative abilities. Less well known is how planarians maintain spatial patterning in long-lived adult animals or how they re-pattern tissues during regeneration. HOX genes are good candidates to regulate planarian spatial patterning, yet the full complement or genomic clustering of planarian HOX genes has not yet been described, primarily because only a few have been detectable by in situ hybridization, and none have given morphological phenotypes when knocked down by RNAi. Results: Because the planarian Schmidtea mediterranea (S. med) is unsegmented, appendage-less, and morphologically simple, it has been proposed that it may have a simplified HOX gene complement. Here we argue against this hypothesis and show that S. med has a total of 13 HOX genes, which represent homologs to all major axial categories, and can be detected by whole-mount in situ hybridization using a highly-sensitive method. In addition, we show that planarian HOX genes do not cluster in the genome, yet 5/13 have retained aspects of axially-restricted expression. Finally, we confirm HOX gene axial expression by RNA-deep-sequencing 6 anterior-to-posterior “zones” of the animal, which we provide as a dataset to the community to discover other axially-restricted transcripts. Conclusions: Freshwater planarians have an unappreciated HOX gene complexity, with all major axial categories represented. However, we conclude based on adult expression patterns that planarians have a derived body plan and their asexual lifestyle may have allowed for large changes in HOX expression from the last common ancestor between arthropods, flatworms, and vertebrates. Using our in situ method and axial zone RNAseq data, it should be possible to further understand the pathways that pattern the anterior-posterior axis of adult planarians.
2016-03-08 | GSE78937 | GEO
Project description:The transcriptome of the planarian Schmidtea mediterranea is not well characterized. We have used RNA-Seq to characterize the transcriptome in both sexual and asexual strains of S. mediterranea from both untreated and irradiated animals. Moreover, we have performed RNA-Seq on RNA purified from FACS sorted neoblasts and differentiated cells. Together these studies expand our understanding of the planarian transcriptome and have identified strain-specific, neoblast-specific, and conserved transcripts. RNA-Seq was performed on RNA isolated from untreated and irradiated S. mediterranea animals from both the sexual and asexual strains, on FACS purified X1 neoblasts, X2 neoblasts, and Xins differentiated cells. One of the raw data files for GSM847465 is missing. The fasta file is provided at http://genome.vcell.uchc.edu/GenomeData02/Graveley_Lab_Public_Data/Planarian/S.mediterranea_SexNIRmRNA3.fa.gz
2012-04-24 | E-GEOD-34326 | biostudies-arrayexpress
Project description:Identification of differentially expressed genes in intestinal phagocytes, compared to non-intestinal cells in Schmidtea mediterranea. Total RNA was isolated from either intestinal phagocytes or non-intestinal cells (control). Four independent biological replicates were conducted with two dye swaps. Labeled targets were hybridized to two oligonucleotide arrays on which 11,521 planarian transcripts were represented.
2012-10-01 | E-GEOD-35565 | biostudies-arrayexpress
Project description:Gene expression domains along the planarian A/P axis
| PRJNA324748 | ENA
Project description:HOX gene complement and expression in the planarian Schmidtea mediterranea
| PRJNA314467 | ENA