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Transcriptional and genome organization changes in HT1080 cells after overexpression of tissue-specific nuclear transmembrane proteins (NETs)

ABSTRACT: Transcriptional and genome organization changes in HT1080 cells after overexpression of tissue-specific nuclear transmembrane proteins (NETs)

PROVIDER: PRJNA343933 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4281390.fastq.gz	Fastqsanger.gz
	SRR4281391.fastq.gz	Fastqsanger.gz
	SRR4281392.fastq.gz	Fastqsanger.gz
	SRR4281393.fastq.gz	Fastqsanger.gz
	SRR4281394.fastq.gz	Fastqsanger.gz

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Similar Datasets

Transcriptional and genome organization changes in HT1080 cells after overexpression of tissue-specific nuclear transmembrane proteins (NETs)

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-12-31 | GSE87228 | GEO

Transcriptome analysis of human HT1080 cells overexpressing full length or soluble nucleoplasmic fragment of NET29/TMEM120A, NET39/PPAPDC3 and NET47/TM7SF2

Project description:The nuclear transmembrane proteins (NETs) NET29/TMEM120A, NET39/PPAPDC3 and NET47/TM7SF2 are able to reposition chromosomes towards/away from the nuclear envelope when overexpressed or knocked down in HT1080 cells. In this study we wanted to investigate the transcriptome changes after transfection of the full length NETs or a nucleoplasmic soluble fragment that does not localise to the nuclear envelope.

2016-12-31 | GSE87150 | GEO

Establishment of tissue-specific genome organisation by muscle-specific nuclear envelope transmembrane proteins (NETs) during mouse C2C12 myoblast differentiation

Project description:Establishment of tissue-specific genome organisation by muscle-specific nuclear envelope transmembrane proteins (NETs) during mouse C2C12 myoblast differentiation

| PRJNA318614 | ENA

Expression data from RECK-overexpressing HT1080 fibrosarcoma cells

Project description:RECK, a glycosylphosphatidylinositol-anchored glycoprotein, inhibits the enzymatic activities of some matrix metalloproteinases (MMP), thereby suppressing tumor cell metastasis; however, the detailed mechanism is still obscure. In this study, we compared the gene expression profiles between mock- and RECK-transfected HT1080 cells. Three established cell lines were selected for RNA extraction and hybridization on Affymetrix microarrays: (1) mock-transfected HT1080 cells, designated as HT1080-Zeo, (2) RECK-overexpressing HT1080 cells, designated as HT1080-RECK, and (3) RECK/4NQ-overexpressing HT1080 cells (in which four N-glycosylation asparagine residues of RECK (Asn86, Asn200, Asn297, and Asn352) were replaced with glutamine residues), designated as HT1080-RECK/4NQ.

2010-04-14 | E-GEOD-21306 | biostudies-arrayexpress

The effect of neutrophil extracellular trap (NETs) on BMDMs

Project description:To investigate the altered gene expression levels in BMDMs treated with or without NETs. Each group had a biological repeat (n=3). Results provide insight into the effect of NETs on BMDMs.

2024-11-27 | GSE268729 | GEO

RNA Sequencing reveals transcriptome profiling of HUVECs in response to NETs ± defibrotide

Project description:We reported the application of RNA sequecing to broadly understand the pathways associated with HUVECs exposed to vehicle, NETs, or NETs + defibrotide. We identified 440 differentially expressed genes (300 upregulated) in HUVECs upon NET stimulation as compared with vehicle. Conversely, there were 229 differentially expressed genes (192 downregulated) when the NETs + defibrotide group was compared to NETs alone.

2021-10-13 | GSE179828 | GEO

Neutrophil Extracellular Traps (NETs) promote macrophage inflammation and impair atherosclerosis resolution in mice with diabetes

Project description:Neutrophil extracellular traps (NETs) promote inflammation and atherosclerosis progression. In diabetes they are increased and impair wound healing, during which inflammation normally resolves. Atherosclerosis regression, a process resembling wound healing, is also impaired in diabetes. Thus, we hypothesized that NETs impede atherosclerosis regression in diabetes through unresolved inflammation. Objective: To investigate in diabetes the effect of NETs on plaque macrophage inflammation and whether NETs reduction improves atherosclerosis regression. Findings: Transcriptomic profiling of plaque macrophages from NET positive and negative areas in Ldlr-/- mice revealed inflammasome and glycolysis pathway upregulation, indicating a pro-inflammatory phenotype. During atherosclerosis regression in non-diabetic mice, plaque NET content decreased. In contrast, in diabetic mouse plaques NETs were enriched and persisted after lipid-lowering. DNase1 treatment (to degrade NETs) of diabetic mice reduced plaque NETs and macrophage inflammation and improved atherosclerosis regression after lipid-lowering. Conclusions: NETs decline during atherosclerosis regression in non-diabetic mice, but persist in diabetes and impair regression by exacerbating macrophage inflammation. DNase1 reduced diabetic plaque NETs and macrophage inflammation, and restored atherosclerosis resolution after lipid-lowering, despite ongoing hyperglycemia. Given that humans with diabetes also exhibit impaired atherosclerosis resolution with lipid-lowering, these data suggest that NETs contribute to the increased CVD risk in this population.

2020-05-12 | GSE145200 | GEO

LaminB1 DamID in HT1080 fibroblasts overexpressing NET29/TMEM120A, NET39/PPAPDC3 or NET47/TM7SF2

Project description:Maps of genomic regions in proximity to the nuclear lamina were determined in untreated HT1080 fibroblasts and HT1080 stable cell lines expressing NET29/TMEM120A, NET39/PPAPDC3 or NET47/TM7SF2 as GFP fusions

2016-12-31 | GSE87148 | GEO

microRNA profiling in different grading of gastroenteropancreatic neuroendocrine tumors (GEP-NETs)

Project description:Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are rare and heterogeneous tumors presenting a wide spectrum of different clinical and biological characteristics. In these tumors, the histological evaluation is a crucial element of clinical management. Currently, tumor grading, determined by Ki-67 staining and mitotic counts, is the most reliable predictor of prognosis. This scoring method is time-consuming and a high reproducibility cannot be achieved. Novel approaches are needed to support histological evaluation and prognosis. In this study, starting from a microarray analysis, we defined the miRNAs signature for poorly differentiated NETs (G3) compared to well differentiated NETs (G1 and G2) consisting of 56 deregulated miRNAs. Moreover, we identified 8 miRNAs that were expressed in all GEP-NETs grades but at different level. Among these miRNAs, we found miR-96-5p that raised its expression levels from grade 1 to grade 3; inversely, its target FOXO1 was decrease from grade 1 to grade 3. Our results reveal that the miRNAs expression profile of GEP-NET correlates their expression with grading showing a potential advantage of miRNA quantification to aid clinicians in the classification of common GEP-NETs subtypes.

2020-08-04 | GSE135034 | GEO

NETOME: The Molecular Characterization of Neutrophil Extracellular Traps (NETs)

Project description:Neutrophils are necessary in mamalian’s life and are the most abundant type of white blood cells in humans with biological roles relevant to inflammation and the entire host response. The release of neutrophil extracellular DNA in innate immune cells provides specific response to bacteria and fungi. Neutrophil Extracellular Traps (NETs) act as antimicrobial agents and activators of immune response through release of the nuclear content into the extracellular space. Although great strides have been made in dissecting cellular and molecular pathways that control NET formation, the exact molecular composition of released NETs has not been elucidated. Here, we open the field of NETOMIC studies through isolation of NETs in combination with shotgun genomics and proteomics. This study reveals the molecular composition of NETs and specific expression regions of NETs induced in a sterile inflammation system. The existence of an in vitro NET isolation model allowed for an unprecedented amount of replicability. Additional studies are needed to verify the specificity of these sequences in the context of human health and disease upon diverse neutrophil microbial challenges.

2022-10-25 | PXD016143 | Pride

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