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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Wound-induced neoblast specialization in S. mediterranea

ABSTRACT: We report the expression of mRNA transcripts in X1 neoblast isolated by FACS followin amputation of the head (anterior wounding) and amputation of the pharyx and tail (posterior wounding) at 0 and 48 hours RNA-sequencing of pre-pharyngeal X1 cells from anterior and posterior facing wounds at 0 and 48 hrs after wounding in S. mediterranea

ORGANISM(S): Schmidtea mediterranea

SUBMITTER: Kellie Kravarik

PROVIDER: E-GEOD-57226 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Neoblast specialization in regeneration of the planarian Schmidtea mediterranea.

Scimone M Lucila ML Kravarik Kellie M KM Lapan Sylvain W SW Reddien Peter W PW

Stem cell reports 20140704 2

Planarians can regenerate any missing body part in a process requiring dividing cells called neoblasts. Historically, neoblasts have largely been considered a homogeneous stem cell population. Most studies, however, analyzed neoblasts at the population rather than the single-cell level, leaving the degree of heterogeneity in this population unresolved. We combined RNA sequencing of neoblasts from wounded planarians with expression screening and identified 33 transcription factors transcribed in ...[more]

PMID: 25254346

Similar Datasets

Wound-induced neoblast specialization in S. mediterranea

Project description:We report the expression of mRNA transcripts in X1 neoblast isolated by FACS followin amputation of the head (anterior wounding) and amputation of the pharyx and tail (posterior wounding) at 0 and 48 hours

2014-08-19 | GSE57226 | GEO

Neoblast expression in head and tail regeneration

Project description:X1 neoblasts (G2/S/M cells) were isolated by FACS from injury site-proximal tissue in a timeseries during head (anterior) and tail (posterior) regeneration in Schmidtea mediterranea 24 samples: 2 treatments (head versus tail regeneration), 3 timepoints (0,24,48,72 hours post amputation), 3 biological replicates each condition

2014-05-01 | E-GEOD-56178 | 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

Three Distinct Phases of Regeneration-Specific Gene Expression in the Axolotl Blastema

Project description:The salamander has the remarkable ability to regenerate its limb after amputation. Cells at the site of amputation form a blastema and then proliferate and differentiate to regrow the limb. To better understand this process, we have performed deep RNA sequencing of the blastema over a time course. We find genes expressed in three phases with a prominent burst in oncogene expression during the first day, blastemal/limb bud genes peaking at 7 to 14 days, and markers for terminal differentiation upregulated later. We compare these expression patterns to those in a mouse digit amputation model to identify genes specific to the regenerative response. We find that limb patterning genes, SALL genes, and genes involved in the proteasome, adult stem cell, embryonic stem cell, retinoid metabolism, and WNT and NOTCH signaling are regeneration-specific. We establish the “Axolomics” Database, which provides a tool for depositing, retrieving, and searching axolotl-related “omic” information. The experiment includes two time course data sets. One is from mouse digit amputation, another is from Axolotl digit amputation

2013-09-01 | E-GEOD-34394 | biostudies-arrayexpress

Comparison between two different Pinus pinaster provenances (RNA-Seq)

Project description:The transcriptome of needles from plants propagated by cuttings and cultured in the same conditions at SERIDAâ??s greenhouse at Villaviciosa (Asturias, Spain) were analyzed. The cuttings are from two different provenances of Pinus pinaster; Leiria (Portugal) and Tamrabta (Morocco). Their transcriptomes were analyzed using high throughput sequencing 4 samples

2015-11-04 | E-GEOD-61923 | biostudies-arrayexpress

Cucumber transcriptome tells story of early fruit development from fruit set through exponential growth

Project description:Early stages of fruit growth from initial set through exponential growth are critical determinants of size and yield, however, there has been little detailed analysis of this phase of development. In this study we combined morphological analysis with 454 pyrosequencing to study gene expression changes occurring in young cucumber fruit at five ages from anthesis through the end of exponential growth. The resulting 1.13 million ESTs were assembled into 27,859 contigs with a mean length of 834 base pairs and a mean of 67 reads per contig. Principal component analysis separated the fruit ages into three groups corresponding with cell division/pre-exponential growth (0 and 4 days post pollination (dpp)), peak exponential expansion (8dpp), and late/post-exponential expansion stages of growth (12 and 16 dpp). Transcripts predominantly expressed at 0 and 4 dpp included homologs of histones, cyclins, and plastid and photosynthesis related genes. The group of genes with peak expression at 8dpp included cytoskeleton, cell wall, and lipid metabolism related genes and phloem specific proteins. This group also was dominated by genes with unknown function or without Arabidopsis homologs, suggesting unique factors contributing to the rapid growth phase in cucurbits. A second shift in gene expression was observed at 12-16dpp, which was characterized by abiotic and biotic stress related genes and significant enrichment for stress related- and developmental- transcription factor gene homologs. Collectively, the gene expression information coupled with morphological analyses tells a progressive story of cell division, development of photosynthetic capacity, cell expansion and fruit growth, phloem activity, protection of the fruit surface, and finally transition away from fruit growth toward defense and maturation. mRNA profiling of early fruit development using 454 sequencing.

2012-07-12 | E-GEOD-39310 | biostudies-arrayexpress

Single-cell analysis reveals prominent classes within the planarian stem cell compartment

Project description:Single cell qPCR analysis identified two prominent expression signatures within the planarian stem cells, the neoblasts. RNAi against zinc finger protein zfp-1 results in elimination of one of the two classes. Worms were treated with RNAi by feeding. X1 or X2 cells were isolated by FACS, or blastemas were dissected. mRNA libraries were sequenced.

2014-09-30 | E-GEOD-58057 | biostudies-arrayexpress

Single cell RNA-seq of tail tissue from regeneration-competent and -incompetent Xenopus laevis tadpoles

Project description:Xenopus laevis tadpoles differ in their regenerative potential according to their developmental stage. Here, we focus on tail regeneration following amputation. By comparing the regenerative response during the naturally occurring regeneration-competent and -incompetent stages, scRNAseq can reveal cell type changes that are required for successful regeneration.

2019-04-23 | E-MTAB-7716 | biostudies-arrayexpress

Bulk ATAC-seq of mouse Plasmodium-specific CD4+ T cells

Project description:Plasmodium-specific CD4+ T cells from mice infected with Plasmodium chabaudi chabaudi AS parasites were recovered at Days 0, 7, and 28 to undergo processing and to generate ATAC-seq dataset (2 independent biological repeats per time point). At Day 28, mice were administered with either saline or artesunate (intermittent artesunate therapy - IAT). Bulk ATAC-seq dataset was analysed to investigate epigenomic landscapes of CD4+ T cells from effector to memory states.

2020-10-14 | E-MTAB-9393 | biostudies-arrayexpress

RNA Seq analysis of sorted Schmidtea mediterranea X1 and Xins cells to identify factors specific to neoblasts

Project description:Adult stem cells are tissue-specific cells with the capacity to self-renew and differentiate to continually replace cells lost to normal physiological turnover or injury. Neoblasts, the planarian stem cells, are widely distributed throughout the body mesenchyme, driving constitutive renewal of tissues during homeostasis and endowing planarians with the remarkable capacity to regenerate wholly from tiny tissue fragments. Neoblasts are the only dividing cells in planarians and are believed to be collectively comprised of both a heterogeneous population of pluripotent cells with broad differentiation potential and also lineage-committed progenitor cells that give rise to specific tissues. Recent technology has allowed one to isolate stem cells so we used a well-established method to isolate planarian stem cells by Hoechst blue staining and flow cytometry. To understand the molecular mechanisms underlying neoblast differentiation, we performed an RNA-Seq analysis of X1 and Xins cells looking at the differentially expressed genes between the two populations. Examine gene expression profiles of adult flatwormâ??s X1 and Xins cell types. The experiment was performed in quadruplicate yielding a total of 8 samples.

2015-12-17 | E-GEOD-73027 | biostudies-arrayexpress

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