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Digital Gene Expression profiling of Schmidtea mediterranea stem cells.

ABSTRACT: The freshwater planarian Schmidtea mediterranea is well known by its amazing regeneration capabilities thanks to the presence of adult stem cells, the neoblasts, the only proliferative cells and responsible for the differentiation in all the cell types of the organism. This study involves the creation of separated transcript libraries from both, isolated neoblasts and differentiated cells, as well as their posterior sequencing and quantification through Digital Gene Expression (DGE) for the characterization of the neoblast transcriptome.

ORGANISM(S): Schmidtea mediterranea

PROVIDER: GSE51681 | GEO | 2015/05/07

SECONDARY ACCESSION(S): PRJNA224556

REPOSITORIES: GEO

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Digital Gene Expression profiling of Schmidtea mediterranea stem cells.

Project description:The freshwater planarian Schmidtea mediterranea is well known by its amazing regeneration capabilities thanks to the presence of adult stem cells, the neoblasts, the only proliferative cells and responsible for the differentiation in all the cell types of the organism. This study involves the creation of separated transcript libraries from both, isolated neoblasts and differentiated cells, as well as their posterior sequencing and quantification through Digital Gene Expression (DGE) for the characterization of the neoblast transcriptome. Three DGE libraries were produced from FACS isolated cell populations X1 (proliferating stem cells, S/G2/M), X2 (a mix of proliferating stem cells and stem cell progeny, G0/G1) and Xin (differentiated cells, G0/G1). Cells were isolated from a pool of 32 regenerating animals two days after being cut off pre- and post-pharingeally to trigger regeneration and neoblast proliferation.

2015-05-07 | E-GEOD-51681 | biostudies-arrayexpress

Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea

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

Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea

2012-04-25 | GSE34326 | GEO

The head-regeneration transcriptome of the planarian Schmidtea mediterranea

Project description:The head-regeneration transcriptome of the planarian Schmidtea mediterranea

2011-07-15 | E-MTAB-607 | biostudies-arrayexpress

Identification of TOR-responsive slow-cycling neoblasts in planarians

Project description:Epimorphic regeneration commonly relies on the activation of quiescent stem cells to drive new cell production. The planarian Schmidtea mediterranea is among the best regenerators in nature, thanks to its large population of adult stem cells, called neoblasts. While neoblasts have long been known to drive regeneration, whether a subset of neoblasts is reserved for this purpose is unknown. Here, we revisited the idea of reserved neoblasts by approaching neoblast heterogeneity from a regulatory perspective. By implementing a new fluorescence-activated cell sorting strategy in planarians, we identified a population of neoblasts defined by low transcriptional activity. These RNAlow neoblasts are relatively slow-cycling at homeostasis and undergo a morphological regeneration response characterized by cell growth at 48 hours post-amputation. At this time, RNAlow neoblasts proliferated in a TOR-dependent manner. Additionally, knockdown of the tumour suppressor Lrig-1, which is enriched in RNAlow neoblasts, resulted in RNAlow neoblast growth and hyperproliferation at homeostasis, and ultimately delayed regeneration. We propose that slow-cycling RNAlow neoblasts represent a regeneration-reserved neoblast population.

2020-12-31 | GSE157860 | GEO

RNA Seq analysis of gene expression during Schmidtea mediterranea embryogenesis, including yolk and adult samples

Project description:Planarian neoblasts are pluripotent, adult somatic stem cells and lineage-primed progenitors required for the production and maintenance of all differentiated cell types, including the germline. Neoblasts, originally defined by Harriet Randolph as undifferentiated, embryonic-like cells residing in the adult parenchyma, are frequently compared to embryonic stem cells yet their developmental origin remains obscure. We investigated the provenance of neoblasts during S. mediterranea embryogenesis, and report that neoblasts arise from an anarchic, cycling piwi-1+ population that is wholly responsible for production of all temporary and definitive organs during embryogenesis. Early embryonic piwi-1+ cells are molecularly and functionally distinct from neoblasts: they express unique cohorts of early embryo enriched transcripts and the cells behave differently than neoblasts in cell transplantation assays. Neoblast lineages, established as organogenesis commences, persist into adulthood, where they act as agents of tissue homeostasis and regeneration.

2016-12-01 | GSE82280 | GEO

Expression analysis of purified intestinal phagocytes in Schmidtea mediterranea

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

RNA sequencing of single cells from the midline posterior extremity in planarian Schmidtea mediterranea

Project description:RNA sequencing of single cells from the midline posterior tip of the tail and posterior blastema in planarian Schmidtea mediterranea identified new posterior-pole enriched genes

2019-05-25 | GSE121047 | GEO

[E-MTAB-607] Transcription profiling by high throughput sequencing of the planarian Schmidtea mediterranea during head regeneration

Project description:The head-regeneration transcriptome of the planarian Schmidtea mediterranea ArrayExpress Release Date: 2011-07-15 Publication Title: The head-regeneration transcriptome of the planarian Schmidtea mediterranea Publication Author List: Thomas Sandmann, Matthias C. Vogg, Suthira Owlarn, Michael Boutros, and Kerstin Bartscherer Person Roles: submitter Person Last Name: Sandmann Person First Name: Thomas Person Mid Initials: Person Email: t.sandmann@dkfz.de Person Phone: +49 6221 42 1954 Person Address: Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany Person Affiliation: German Cancer Research Center

2012-01-20 | GSE30996 | GEO

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

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