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RNAseq in whole freshwater planarians, Schmidtea mediterranea, following RNAi of the transcription factors lhx1/5-1 and pitx.

ABSTRACT: Freshwater planarians can be used as a model to investigate neuronal function and maintenance in adults in vivo. We knocked down expression for 2 transcription factors, then sequenced resulting animals to examine transcriptional changes that may have occurred.

ORGANISM(S): Schmidtea mediterranea

PROVIDER: GSE47348 | GEO | 2013/05/31

REPOSITORIES: GEO

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RNAseq in whole freshwater planarians, Schmidtea mediterranea, following RNAi of the transcription factors lhx1/5-1 and pitx.

Project description:Freshwater planarians can be used as a model to investigate neuronal function and maintenance in adults in vivo. We knocked down expression for 2 transcription factors, then sequenced resulting animals to examine transcriptional changes that may have occurred. There are 3 triplicated conditions: control(RNAi) using the unc22 gene from C. elegans, lhx1/5-1(RNAi), and pitx(RNAi). Worms were fed RNAi for each gene 5 times over 12 days then were collected 12 days later. Approximately 50 million single-end reads were performed on each sample.

2013-05-31 | E-GEOD-47348 | biostudies-arrayexpress

Transcriptional profiling of Schmidtea mediterranea planarians (smed-runt-1 RNAi vs. control RNAi)

Project description:Transcriptional profiling of Schmidtea mediterranea planarians that have been subjected to 2 weeks of runt-1 or control RNAi, amputated and RNA was directly collected at 5min, 9h, and 24h, or neoblasts (X1) were isolated from 9h wounded animals and subsequently RNA was extracted

2012-04-30 | GSE36869 | GEO

Transcriptional profiling of Schmidtea mediterranea planarians (smed-runt-1 RNAi vs. control RNAi)

2012-04-29 | E-GEOD-36869 | biostudies-arrayexpress

HOX gene complement and expression in the planarian Schmidtea mediterranea

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

RNAseq in the whole whole freshwater planarian, Schmidtea mediterranea, following RNAi of lhx1/5-1, pitx or yorkie

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-10-03 | GSE73701 | GEO

Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identifies major cell types and pathway conservation

Project description:Background: In the Lophotrochozoan superphylum, few organisms have the capacity for rapid testing of gene function and single-cell transcriptomics as the freshwater planarian. The species Schmidtea mediterranea in particular has become a powerful model to study adult stem cell biology and mechanisms of regeneration. Despite this, systematic attempts to define gene complements and their annotations are lacking, restricting comparative analyses that detail the conservation of biochemical pathways and identify lineage-specific innovations. Results: In this study we compare several transcriptomes and define a robust set of 35,232 transcripts. From this, we perform systematic gene annotations and undertake a genome-scale metabolic reconstruction for S. mediterranea. Cross-species comparisons of gene content identify both conserved, lineage-specific, and expanded gene families, which may contribute to the regenerative properties of planarians. In particular, we find that TRAF and cadherin gene families have been greatly expanded in planarians. We further provide a single-cell RNA-sequencing analysis of 2000 cells, revealing both known and novel cell-types defined by unique signatures of gene expression. Amongst these were a novel mesenchymal cell population as well as a cell type involved in eye regeneration. Integration of our metabolic reconstruction further reveals the extent to which a given cell types have adapted energy and nucleotide biosynthetic pathways to support their specialized roles. Conclusions: In general, S. mediterranea displays a high level of gene and pathways conservation with other model systems, rendering it as a viable model to study the roles of these pathways in stem cell biology and regeneration.

2018-08-01 | GSE115280 | GEO

Schmidtea mediterranea

Project description:Unirradiated vs. irradiated wounded planarians

| PRJNA157277 | ENA

Identification of dysregulated transcripts in nkx2.2(RNAi) planarians.

Project description:Nkx2.2 is an intestine-enriched transcription factor required for regeneration in planarians. The goal of this study was to identify differentially expressed transcripts in uninjured nkx2.2(RNAi) planarians.

2022-05-24 | GSE174228 | GEO

Schmidtea mediterranea

Project description:Gene Expression Profiles of Planarians after 6,000 Rads Irradiation

| PRJNA151119 | ENA

Identification of dysregulated transcripts in apob-1(RNAi);apob-2(RNAi) planarians

Project description:ApoB-1 and ApoB-2 are intestine-enriched regulators of lipoprotein secretion in planarians. The goal of this study was to identify differentially expressed transcripts in uninjured apob-1(RNAi);apob-2(RNAi) double knockdown planarians relative to egfp(RNAi) control animals.

2022-05-24 | GSE174227 | GEO

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