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Schmidtea mediterranea strain:CIW4

ABSTRACT: Transcriptional profiling of soxB1-2 RNAi planarians

PROVIDER: PRJNA432445 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7760060.fastq.gz	Fastqsanger.gz
	SRR7760070.fastq.gz	Fastqsanger.gz
	SRR7760061.fastq.gz	Fastqsanger.gz
	SRR7760071.fastq.gz	Fastqsanger.gz
	SRR7760062.fastq.gz	Fastqsanger.gz

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Schmidtea mediterranea

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

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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

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

Schmidtea mediterranea

Project description:Unirradiated vs. irradiated wounded planarians

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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.

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Schmidtea mediterranea strain:CIW4

Project description:Schmidtea mediterranea strain:CIW4 Transcriptome or Gene expression

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Schmidtea mediterranea strain:CIW4

Project description:Schmidtea mediterranea CIW4 Transcriptome

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Schmidtea mediterranea strain:CIW4

Project description:Schmidtea mediterranea strain:CIW4 Genome sequencing and assembly

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Schmidtea mediterranea strain:CIW4

Project description:PIWI function