ABSTRACT: RNA Seq analysis of neoblasts from Schmidtea mediterranea treated with RNAi against zfp1, p53, or unc22 to identify factors involved in neoblast differentiation.
Project description:RNA Seq analysis of Schmidtea mediterranea treated with RNAi against chd4, p53, or unc22 to identify factors involved in neoblast differentiation.
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.
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
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.
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.
Project description:Investigation of whole genome gene expression level changes in nanos(RNAi) Schmidtea mediterranea, compared to control animals. nanos(RNAi) animals are devoid of germ cells The samples analyzed in this study are further described in Wang, Y., Stary, JM., Wilhelm, JE. and Newmark, PA. 2010. A eight chip study using total RNA recovered from asexual nanos(RNAi), asexual control, juvenile sexual nanos(RNAi), and juvenile sexual control 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.
Project description:Investigation of whole genome gene expression level changes in nanos(RNAi) Schmidtea mediterranea, compared to control animals. nanos(RNAi) animals are devoid of germ cells The samples analyzed in this study are further described in Wang, Y., Stary, JM., Wilhelm, JE. and Newmark, PA. 2010.
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
