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Effect of externally applied concave and convex curvature for 24 hours with continued duam SMAD inhibition (dSMADi) on human embryonic cell line H9 after 48 hours of dSMADi induction to attain early neuroepithelial features

ABSTRACT: Effect of externally applied concave and convex curvature for 24 hours with continued duam SMAD inhibition (dSMADi) on human embryonic cell line H9 after 48 hours of dSMADi induction to attain early neuroepithelial features

PROVIDER: PRJNA1040314 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26830662_1.fastq.gz	Fastqsanger.gz
	SRR26830662_2.fastq.gz	Fastqsanger.gz
	SRR26830663_1.fastq.gz	Fastqsanger.gz
	SRR26830663_2.fastq.gz	Fastqsanger.gz
	SRR26830664_1.fastq.gz	Fastqsanger.gz

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Effect of externally applied concave and convex curvature for 24 hours with continued duam SMAD inhibition (dSMADi) on human embryonic cell line H9 after 48 hours of dSMADi induction to attain early neuroepithelial features

Project description:To investigate the transcriptional change induced by externally applied concave and convex curvature, the former of which displayed tissue-level morphological change, human embryonic cell line H9 maintained for pluripotency with mTeSR1 for 72 hours and then induced to have early neuroepithelial features with N2B27 media containing 10 μM of SB431542 and 0.1 μM of LDN (dual SMAD inhibition) for 48 hours. Then along with the continued dual SMAD inhibition, plate curving cell culture of either concave or convex conformation for 24 hours was applied on the cell culture, at the end of which time point cell pellet was collected for bulk RNA sequencing.

2023-11-19 | GSE247786 | GEO

Regulation of corneal stromal cell behavior by modulating curvature using a hydraulically-controlled organ chip array

Project description:Cornea exhibits distinct curvature-dependent mechanical environments that influence stromal cell phenotype and extracellular matrix remodeling. In this study, we employed a hydraulically-controlled cornea-on-a-chip platform to systematically vary curvature and examine transcriptional and phenotypic responses of human corneal keratocytes. RNA sequencing revealed differential expression profiles associated with curvature states that mimic pathological conditions such as cornea plana and keratoconus. Curvature-dependent regulation of extracellular matrix genes, cytoskeletal organization, and signaling pathways was validated with qPCR and immunostaining. These findings provide transcriptomic insights into how corneal tissue geometry contributes to disease progression and may inform future therapeutic strategies for corneal ectatic disorders.

2025-09-30 | GSE308374 | GEO

Epigenome analysis of low-grade neuroepithelial tumors with FGFR2 fusions

Project description:Genome-wide DNA methylation profiling of 8 low-grade neuroepithelial tumors (LGNET) with FGFR2 fusions with various histologic diagnoses including ganglioglioma, multinodular and vacuolating neuronal tumor (MVNT), low-grade glioneuronal tumor NOS, and polymorphous low-grade neuroepithelial tumor of the young (PLNTY). The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of 8 low-grade neuroepithelial tumors with FGFR2 fusions.

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Project description:WDR12 is a ribosome biogenesis factor known to be expressed in Optic tectum Neuroepithelial cells, we define the transcriptome profile of the optic tectum neuroepithelial cells, by cell-sorting followed by RNA-seq (Illumina technology).

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Epigenome analysis of low-grade neuroepithelial tumors with FGFR1 alterations

Project description:Genome-wide DNA methylation profiling of 30 low-grade neuroepithelial tumors with FGFR1 alterations including rosette-forming glioneuronal tumor, pilocytic astrocytoma, dysembryoplastic neuroepithelial tumor, and extraventricular neurocytoma. The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of 30 low-grade neuroepithelial tumors with FGFR1 alterations including kinase domain tandem duplication, in-frame fusion with TACC1, and hotspot missense mutation within the intracellular tyrosine kinase domain.

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Transcription profiling of human embryonic stem cells and neuroepithelial cells

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CINCINNATA Controls Surface Curvature of Antirrhinum Leaf by Coordinated and Direct Activation of Cytokinin and Auxin Signaling

Project description:Mutations in the CINCINNATA gene in Antirrhinum and its orthologues in Arabidopsis cause negative surface curvature in leaves due to excess marginal growth. CIN-like genes code for TCP transcription factors and are expressed in a broad zone of a growing leaf somewhat distal to the proliferation zone. Although a few TCP targets are known, the role of CIN-like TCP genes in regulating leaf curvature has remained unclear. We have compared the global transcription profile of wild type and cincinnata mutant to identify its targets. By combining DNA-protein interaction, chromatin immunoprecipitation and RNA in situ hybridization, we show that CIN maintains surface flatness by regulating signaling or level of major plant hormones. CIN promotes cytokinin signaling directly and GA level indirectly, in accelerating maturity in leaf cells along the tip-to-base direction. In addition, CIN suppresses auxin signaling more at the margin than centre by establishing a margin-to-medial expression gradient of a homologue of the auxin suppressor IAA3. Our results uncover an underlying mechanism in a developing leaf that controls maturity of leaf and its surface curvature. Considering the conservation of CIN-like genes and their function in leaf morphogenesis in multiple plant species, it is likely that such mechanism is evolutionarily conserved. Two color Experiment, Organism: Arabidopsis thaliana and Antirrhinum. Arrays Used: 1. Agilent Arabidopsis thaliana Gene expression Microarray 22k (AMADID: 013324) 2. Agilent Custom Arabidopsis thaliana 4x44k Gene Expression (AMADID: 015226) 3. Agilent custom Antirrhinum 4x44k Gene expression (AMADID: 016341) designed by Genotypic Technology Private Limited.

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Multiome experiment of the neuroepithelial stage of brain organoid developement

Project description:To investigate the heterogeneity during the neuroepithelial stage of organoid development, we performed a multiome experiment on day 15-18 old brain organoids

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CINCINNATA Controls Surface Curvature of Antirrhinum Leaf by Coordinated and Direct Activation of Cytokinin and Auxin Signaling

2013-05-01 | GSE40621 | GEO

A direct link between Prss53, hair curvature, and skeletal dysplasia

Project description:PRSS53, a member of the membrane-anchored serine proteases, hydrolyzes peptide bonds and is highly expressed in the hair follicle IRS, medulla, precortex and some melanocytes1. Previous studies reported that Prss53 is a psoriasis susceptibility locus and is linked to systemic lupus erythematosus, suggesting its potential roles in skin function2. The Q30R SNP in Prss53 may influence hair shape and is involved in the human variation of head hair shape among different continental groups1. In addition, ENaC activity is regulated by the activity of a channel-activating protease of Prss8 (a homologous gene of Prss53), implying the Prss53 may have an indispensable role in ion channel activity3.The triggering of hair curvature is clearly related to symmetry or asymmetry axis formation in follicles and includes Wnt, TGFβ, BMP, Shh and FGFs, etc. In particular, the Wnt/Ca2+ and Wnt/planar cell polarity (PCP) pathways are additional novel mechanisms that affect hair shape4. Furthermore, disruptions in calcium metabolism may contribute to a wide variety of clinical symptoms, including osteoporosis, osteolysis, nephrocalcinosis and adynamie5.Here, we successfully generated Prss53-deficient rabbits. These rabbits exhibited curved hair, severe skeletal malformation and disrupted calcium metabolism. Altogether, these data suggest that Prss53 play an important role in calcium metabolism and provide the first direct evidence that Prss53 functions in hair curvature shape and skeletal dysplasia.

2019-12-04 | GSE141384 | GEO

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