Zebrafish nephrogenic stem cells: lhx1a vs cdh17
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ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE24803 | GEO | 2011/11/01
SECONDARY ACCESSION(S): PRJNA132297
REPOSITORIES: GEO
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Project description:Transcriptional profiling of zebrafish nephrogenic stem cells (lhx1a+) vs. zebrafish renal tubular cells (cdh17+): 2 color design, 3 biological replicates Two-condition experiment, renal tubule vs. nephrogenic stem cells. 3 biological replicates
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Project description:Genome wide DNA methylation profiling of normal kidney (n=36), nephrogenic rest (n=22) and Wilms tumour (n=37) was performed using the Illumina 450k array. Two papers were composed after analysis of this data (1) describes comparative analysis of 22 matched normal kidney-Wilms tumour pairs which identified biomarker differentially methylated regions (DMRs) that could be detected in patient blood; (2) describes comparative analysis of 20 matched trios which identified changes in methylation associated with progression from the precursor lesion towards tumourigenesis. Bisulfte converted DNA from 95 samples of normal kidney, nephrogenic rest and Wilms tumour was hybridised to Illumina HumanMethylation450 bead chips.
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Project description:Human pluripotent stem cells (hPSC) provide a possible source for generation of kidney cells and organoids applicable in regenerative medicine, disease modeling and drug screening. By analyzing the effect of different factors on renal differentiation, we established an 8-day-protocol that steered hPSCs to the renal lineage by a step-wise process, segmented into mesoderm induction, intermediate mesoderm specification and metanephric induction outlining renal organogenesis. The differentiated cells contain populations of SIX2+/CITED1+ metanephric mesenchyme- (MM) and of HOXB7+/GRHL2+ ureteric bud (UB)-like cells at the end of 6 days. Transcriptome analysis corroborated that the in vitro generated precursor cell types at day 8 resemble their renal vesicle counterparts in vivo. The cells were further differentiated in 2-dimensional culture into podocyte- and diverse tubular epithelial-like cell types, showing their nephrogenic potential. In 3-dimensional culture, the progenitors gave rise to renal vesicles, and upon mouse embryonic kidney re-aggregation they form tubular structures.
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Project description:In order to study the effect of mesenchymal stem cells on miRNAs in renal tubular epithelial cells during renal fibrosis, and to find new treatment methods for renal fibrosis, we used TGF-β1 to stimulate mouse tubular epithelial cells, co-cultured with mesenchymal stem cells for 48 hours, and collected renal tubular epithelial cells .The renal tubular epithelial cells that were only stimulated by TGF-β1 were used as a control group. High-throughput miRNA sequencing was used to detect the increased and decreased miRNAs after co-culture.
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Project description:Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex-specific behavioral variation particulary in response to stress and anxiety-inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish, this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA-sequencing (4 biological replicates per strain further subdivided into 2 biological replicates per sex) we analyzed the whole-brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences (e.g. behavioral or morphological) of the strains. Using a balanced block design, all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads (approximately 52 million reads per biological replicate) were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic (e.g. morphological, behavioral) variation in zebrafish.
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Project description:Exposure experiments with the non-aromatizable fish androgen, 11-ketotestosterone in the range of 0.05-5000 nM were conducted in order to identify potential androgen-responsive genes in zebrafish embryos by microarray analysis. Zebrafish embryos were treated from 96 hpf to 120 hpf in a single experiment with three controls (embryonic medium). Microarray studies were performed using a Custom 8x60k Gene Expression Microarrays (Amadid G4102A, based on the ensembl zebrafish genome version 3) from total RNA with low input labelling and hybridization kit (Agilent Technologies) and one-color design according to the manufacturer instructions. Fluorescent intensities of individual microarray spots were extracted using the Agilent Feature Extraction software. Raw microarray data were converted to log2 values and quantile-normalized. For further statistical analysis, fold changes in relation to the mean of the controls were calculated for each treatment.
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Project description:Genome wide DNA methylation profiling of normal kidney (n=36), nephrogenic rest (n=22) and Wilms tumour (n=37) was performed using the Illumina 450k array. Two papers were composed after analysis of this data (1) describes comparative analysis of 22 matched normal kidney-Wilms tumour pairs which identified biomarker differentially methylated regions (DMRs) that could be detected in patient blood; (2) describes comparative analysis of 20 matched trios which identified changes in methylation associated with progression from the precursor lesion towards tumourigenesis.
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Project description:The study comprises various components: Samples TD: We aims to screen out different gene expression profile in donor biopsies after revascularization , We aims to predict renal allograft dysfunction early after transplantation. Samples AR, ATN, Tx: We aim to screen out different gene expression profile in acute rejection on the kidney. We aim to screen out different gene expression profile in acute tubular necrosis on the kidney. Results from the various study components can help to diagnose renal allograft dysfunction with different causes by distinct gene expression profile. Keywords: acute rejection, acute tubular necrosis, donor biopsies, renal allograft dysfunction Samples AR1-AR17: This study has been accomplished with 17 patients of acute rejection on the kidney.Technical replicates: 2 replicates Samples ATN1-ATN5: This study has been accomplished with 5 patients of acute tubular necrosis on the kidney. Technical replicates: 2 replicates Samples Tx1-Tx14: This study has been accomplished with 14 patients of stable renal function on the kidney.Tecnical replicates:2 replicates(except Tx12) Samples TD1-TD12: This study has been accomplished with 12 patients of donor tissue with stable function early after transplantation on the kidney.Technical replicates: 2 replicates Samples TD13-TD21: This study has been accomplished with 9 patients of donor tissue with renal dysfunction early after transplantation on the kidney.Technical replicates: 2 replicates
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