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

ABSTRACT: 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.

ORGANISM(S): Schmidtea mediterranea

PROVIDER: GSE34326 | GEO | 2012/04/25

SECONDARY ACCESSION(S): PRJNA151483

REPOSITORIES: GEO

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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

Digital Gene Expression profiling of Schmidtea mediterranea stem cells.

2015-05-07 | GSE51681 | GEO

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

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

Molecular markers to characterize the hermaphroditic reproductive system of the planarian Schmidtea mediterranea

Project description:Investigation of differences in gene expression between two strains of the planarian Schmidtea mediterranea. The sexual strain are cross-fertilizing hermaphrodites with reproductive organs that develop post-embryonically and the asexual strain reproduces exclusively by transverse fission and fail to develop reproductive organs. A two chip study using total RNA recovered from asexual and sexual animals. Each chip measures the expression level of 16,797 ESTs from S. mediterranea with 10 60-mer probe pairs (PM/MM) per gene, with two-fold technical redundancy.

2011-11-01 | E-GEOD-32450 | biostudies-arrayexpress

Molecular markers to characterize the hermaphroditic reproductive system of the planarian Schmidtea mediterranea

2011-11-01 | GSE32450 | 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

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

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