Similar Datasets
Project description:Bulk RNAseq was performed using P4 human dermal lymphatic endothelial cells (HDLECs)
2022-12-31 | GSE212743 | GEO
Project description:Bulk RNAseq was performed using P4 human dermal lymphatic endothelial cells (HDLECs)
2024-06-30 | GSE243983 | GEO
Project description:Purpose: Zinc Finger MIZ-Type Containing 1 (Zmiz1) is a member of the PIAS family of protein and function as a transcriptional coactivator of Notch, Androgen Receptor (AR), p53, Estrogen Receptor (ER), and Smad3/4 . Despite Zmiz1 critical role in angiogenesis, its role in lymphatic vasculature is unknown. Here, we use HDLECs cell line to profileepigenetic changes upon Zmiz1 knockdown using siRNA. Methods: ATAC sequencing library was prepared as per manufacturer instruction (Active Motif, 53150). Briefly, intact nuclei were isolated from control and Zmiz1 siRNA transfected HDLECs. Samples were treated with a hyperactive Tn5 transposase which tag the target DNA with sequencing adapters and fragment the DNA simultaneously. Library was then quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific, Q32851) and verified using the Bioanalyzer DNA High Sensitivity Assay Kit (Agilent, 5067-4626). Validated samples were sequenced using the NextSeq1000/2000 P2 Reagents (100 Cycles) v3 (Illumina, 20046811) on a Nextseq1000/2000. Resulting sequencing data were analyzed using basepairtech ATAC-Seq pipeline (www.basepairtech.com). Briefly, sequenced reads were aligned to the human (hg19) reference genome using Bowtie2. ATAC-Seq peaks and differentially accessible regions were quantified using MACS2 and DESeq2. Results: ATAC seq peaks analysis using MACS2 identified 576 peaks of which are mostly located in intergenic regions followed by introns. We found significantly reduced open chromatin near Prox1 loci upol loss of Zmiz1. Conclusions: We identify Zmiz1 regulates chromatin accessibility near Prox1 genomic loci in lymphatic endothelial cells
2023-11-29 | GSE225130 | GEO
Project description:Purpose: Zinc Finger MIZ-Type Containing 1 (Zmiz1) is a member of the PIAS family of protein and function as a transcriptional coactivator of Notch, Androgen Receptor (AR), p53, Estrogen Receptor (ER), and Smad3/4 . Despite Zmiz1 critical role in angiogenesis, its role in lymphatic vasculature is unknown. Here, we use HDLECs cell line to profile transcriptional changes upon Zmiz1 knockdown using siRNA. Methods: Total RNA was extracted from control and Zmiz1 siRNA transfected HDLECs using GeneJET RNA Purification Kit (Thermo Fisher Scientific, K0732) following the manufacturer instructions. RNA concentration and RNA integrity (RIN) number were determined using Qubit RNA High Sensitivity Assay Kit (Thermo Fisher Scientific, Q32852) and Bioanalyzer RNA 6000 Nano assay kit (Agilent, 5067-1511) respectively. RNA library was prepared using TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) according to the manufacturer instructions. mRNA library was quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific, Q32851) and verified using the Bioanalyzer DNA1000 assay kit (Agilent, 5067-1505). Verified samples were sequenced using the NextSeq1000/2000 P2 Reagents (200 Cycles) v3 (Illumina, 20046812) on a Nextseq1000/2000. Sequenced reads were aligned to the human (hg19) reference genome with RNA-Seq alignment tool (STAR aligner). The aligned reads were used to quantify mRNA expression and determine differentially expressed genes using the RNA-Seq Differential Expression tool (version 1.0.1). Both alignment and differential expression analysis were performed using the tools in the illumina BaseSpace Sequence Hub. Results: We found 2,228 differentially expressed genes of which 1,115 genes were upregulated while 1,113 genes were downregulated. Downregulated genes were enriched in biological processes such as lymph vessel development, cell migration and heart valve development. Conclusions: We identify Zmiz1 regulates Prox1 in lymphatic endothelial cells
2023-11-29 | GSE225057 | GEO
Project description:We analyzed genome-wide transcriptional changes induced by siYAP/TAZ and YAP5SA, using RNA-seq analysis of HDLECs in order to highlight the importance of Hippo/YAP signaling pathway in lymphatic development and maintenance. Here, we report that YAP/TAZ activity is essential for the appropriate lymphatic development and maintenance.
2019-03-03 | GSE116114 | GEO
Project description:To determine how PGE2 treatment affects HDLECs, we treated cultured HDLECs with either a vehicle or 500 nM dmPGE2 for 16 hours
2023-09-12 | GSE223854 | GEO
Project description:We analyzed genome-wide transcriptional changes induced by siPROX1 and siTIE2, using RNA-seq analysis of HDLECs in order to highlight the importance of Ang-Tie2 system in SC and lymphatic development. Here, we report that coordination between both Ang1- and Ang2-signaling via Tie2 and Prox1 activity are essential for the appropriate formation of SC during development and maintenance of SC integrity.
2017-09-01 | GSE83299 | GEO
Project description:Angiopoietin-Tie1 signaling is required for lymphatic vascular integrity and both ANGPT2 and TIE1 genetic variants have been associated with lymphedema in patients1, 2. Concurrent with growth-factor signaling, mechanical forces sensed by lymphatic endothelial cells (LECs) are also needed to regulate lymphatics3, 4. How these two pathways might interact in the lymphatic system is unknown. Here, we identified a regulatory network in LECs linking activation of the mechanosensory channel, PIEZO1 to Angiopoietin-Tie signaling and repression of a downstream FOXO1 transcriptional response. RNAseq analysis of dermal LECs from Tie1-deficient embryos showed persistent FOXO1 activity with downregulation of LEC-associated genes including Ccl21a, Foxc2, Gata2 and Gja4, as well as increased expression of the mechanosensory channel, Piezo1. Activation of PIEZO1 in human dermal LECs (HDLECs) by the small molecule agonist, Yoda1, triggered exocytosis of the Tie ligand, Angiopoietin-2 (ANGPT2), activation of Tie/AKT/PI3K signaling and export of FOXO1 out of the nucleus. Our data identify a novel molecular pathway linking mechano-transduction to ANGPT2-Tie1 activity and dynamic modulation of FOXO1 activity needed for patterning and function of the lymphatic system
2024-03-05 | GSE211849 | GEO
Project description:M-NM-2-catenin activity of dermal cells is crucial for hair follicle neogenesis and strongly suggest that transcriptional target genes of M-NM-2-catenin pathway are essential for maintaining trichogenicity of dermal cells. We used microarrays to identify genes targeted by the M-NM-2-catenin pathway that are essential for maintaining the trichogenicity of dermal cells. Freshly isolated dermal cells from the dorsal skins of C57BL/6 neonates (P0) were cultured for 24 hours and transfected with either control siRNA or M-NM-2-catenin specific siRNAs (M-NM-2-catenin siRNA) at a final concentration of 10 nM for 48 hours followed by RNA extraction and hybridization on Affymetrix microarrays.
2013-09-03 | E-GEOD-50525 | biostudies-arrayexpress
Project description:Analysis of ex vivo isolated lymphatic endothelial cells from the dermis of patients to define type 2 diabetes-induced changes. Results preveal aberrant dermal lymphangiogenesis and provide insight into its role in the pathogenesis of persistent skin inflammation in type 2 diabetes. The ex vivo dLEC transcriptome reveals a dramatic influence of the T2D environment on multiple molecular and cellular processes, mirroring the phenotypic changes seen in T2D affected skin. The positively and negatively correlated dLEC transcripts directly cohere to prolonged inflammatory periods and reduced infectious resistance of patients´ skin. Further, lymphatic vessels might be involved in tissue remodeling processes during T2D induced skin alterations associated with impaired wound healing and altered dermal architecture. Hence, dermal lymphatic vessels might be directly associated with T2D disease promotion. Global gene expression profile of normal dermal lymphatic endothelial cells (ndLECs) compared to dermal lymphatic endothelial cells derived from type 2 diabetic patients (dLECs).Quadruplicate biological samples were analyzed from human lymphatic endothelial cells (4 x diabetic; 4 x non-diabetic). subsets: 1 disease state set (dLECs), 1 control set (ndLECs)
2012-06-01 | E-GEOD-38396 | biostudies-arrayexpress