Human corneal endothelial cells, iPS cells, CECSi cells, and neural crest cells
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PROVIDER: PRJNA738948 | ENA |
REPOSITORIES: ENA
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Project description:Transcriptional profiling of human iPS cells, CECSi cells and iPS-derived neural crest cells (NCC) comparing human corneal endothelial cells (HCE)
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Project description:Purpose: The goal of this study was to evaluate changes in the transcriptome profile during periocular neural crest differentiation into corneal endothelium and keratocytes. Methods: RNA profiles of chick embryonic day (E3) periocular neural crest, E5 corneal endothelium, and E7 corneal endothelium plus keratocytes were generated in triplicate by deep sequencing using Illumina HS4000. Bowtie2 and HISAT were used to map clean reads to reference gene and genome, respectively. An average mapping ratio of 76.26% to the reference gene and 93.10% to the genome were generated with Galgal5 reference assembly.Transcripts were normalized and presented as Fragments Per Kilobase Million (FPKM). Differentially expressed genes between pNCvsEn and pNCvsKEn were examined. Expression of some candidate genes was validated by in situ hybridization. Results: 790 transcripts were enriched between pNC and En, and 865 transcripts were enriched between pNC and KEn. Enriched transcripts correspond with KEGG pathways involved in cell proliferation, synthesis of extracellular matrix, focal adhesion, metabolism, and cancer. The RNA-Seq data serves as platform for further analyses of the molecular networks involved in NCC differentiation into corneal cells, and provides insights into genes involved in corneal dysgenesis and adult diseases.
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Project description:Gene expression profiles in SOX10-deficient human iPS cell-derived neural crest cells
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Project description:Human corneal endothelial cells (HCEC) form a monolayer by adhering tightly through their intercellular adhesion molecules. Located at the posterior corneal surface, they maintain corneal translucency by dehydrating the corneal stroma, mainly through the Na+- and K+-dependent ATPase (Na+/K+-ATPase). Because HCEC proliferative activity is low in vivo,we tried to activate proliferation of HCEC by inhibiting cyclin-dependent kinase inhibitors.We have here demonstrated microarray data of transduced human corneal endothelial cell lines. Affymetrix human U133 plus 2.0 array was used to transcriptionally profile to compare cultured human corneal endothelial cells and transduced human corneal endothelial cells.
2011-10-29 | E-GEOD-30781 | biostudies-arrayexpress
Project description:RNA-Seq Analysis of Periocular Neural Crest and Embryonic Corneal Transcriptomes
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Project description:Human corneal endothelial cells (HCEC) form a monolayer by adhering tightly through their intercellular adhesion molecules. Located at the posterior corneal surface, they maintain corneal translucency by dehydrating the corneal stroma, mainly through the Na+- and K+-dependent ATPase (Na+/K+-ATPase). Because HCEC proliferative activity is low in vivo,we tried to activate proliferation of HCEC by inhibiting cyclin-dependent kinase inhibitors.We have here demonstrated microarray data of transduced human corneal endothelial cell lines.
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Project description:Cells were isolated from mouse embryonic neural crest stem cells at culture day 2 (NCSC), from day 7 in vitro differentiated progeny (NCP) and day 2 epidermal neural crest stem cells from bulge explants of adult whisker follicles (EPI-NCSC). Keywords: LongSAGE embryonic neural crest stem cells at culture day 2 (NCSC), from day 7 in vitro differentiated progeny (NCP) and day 2 epidermal neural crest stem cells from bulge explants of adult whisker follicles (EPI-NCSC).
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Project description:Neural crest (NC) cells contribute to the development of many complex tissues. The abnormal development of NC cells accounts for a number of congenital birth defects. Generating NC cells, and more specifically NC subpopulations such as cranial, cardiac, and trunk NC cells from human induced pluripotent stem (iPS) cells and human embryonic stem (ES) cells presents a valuable tool to model and study human NC development and disease. Here we provide a robust, efficient, and reproducible protocol for the differentiation of human iPS and ES cells into NC cells. The protocol has been validated in multiple human pluripotent stem cell lines and yields relatively pure NC cell populations in eight days. The resulting cells can be propagated and retain NC marker expression over multiple passages. The NC cells show proper cell specification and can develop into NC-derived cell lineages including smooth muscle cells, peripheral neurons, and Schwann cells. Additionally, the NC cells are functional and migrate to appropriate chemoattractants such as SDF-1, Fgf8b, BMP2, and Wnt3a. Importantly, this method generates all NC subpopulations (cranial, cardiac, and trunk) providing a great advantage to readily available NC differentiation methods. Neural crest cells derived from human induced pluripotent stem cells were profiled using Affymetrix Gene 1.0 arrays to identify differential gene expression changes and alternative exons from the open-source software AltAnalyze. An FDR adjusted emperical Bayes moderated t-test p < 0.05 was used to identify differentially expressed Ensembl genes and GO-Elite used to identify biologically relevant, Ontology, pathway and gene-set categories. Alternative exons were obtained using the FIRMA analysis option and default thresholds. Other array neural crest array and RNA-Seq dataset were compared to this to identify common and distinct regulatory mechanisms.
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Project description:This dataset contains proteomic profiles of Descemet's membrane (DM) with corneal endothelial cells derived from patients with Fuchs endothelial corneal dystrophy (FECD) and non-FECD subjects by shotgun proteomics. FECD is the most common inherited corneal disease. Fibrillar focal excrescences, called guttae, and corneal edema due to corneal endothelial cell death result in progressive vision loss. Our dataset indicated that 32 distinctive molecules were expressed only in the FECD-DM but not in the DM of the control subject, possibly having important roles in the pathophysiology of FECD.
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