Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of human sinusoidal endothelial cells, hepatocyte

ABSTRACT: We report the transcriptome human primary hepatocytes and liver sinusoidal endothelial cells. Hepatocytes were obtained from commercial sources. LSECs were isolated based on the coexpression of Tie2 and CD32b, te strategy of purification controlled by RNA-Seq.

ORGANISM(S): Homo sapiens

PROVIDER: GSE43984 | GEO | 2015/01/01

SECONDARY ACCESSION(S): PRJNA188295

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome analysis of human sinusoidal endothelial cells, hepatocyte

Project description:We report the transcriptome human primary hepatocytes and liver sinusoidal endothelial cells. Hepatocytes were obtained from commercial sources. LSECs were isolated based on the coexpression of Tie2 and CD32b, te strategy of purification controlled by RNA-Seq. Comparison of the expression of the Tie-2, CD32b, SELP, FVIII, VWF, Alb, Fg, F7genes

2015-01-01 | E-GEOD-43984 | biostudies-arrayexpress

MicroRNA expression in male rat hepatocytes and liver sinusoidal endothelial cells (LSECs)

Project description:We determined the microRNA expression profiles of the hepatocytes and liver sinusoidal endothelial cells (LSECs) isolated from nontreated rats.

2017-12-11 | GSE97229 | GEO

Transcriptome of human liver cells and culture-activated hepatic stellate cells

Project description:The molecular determinants of a healthy human liver cell phenotype remain largely uncharacterized. In addition, the gene expression changes associated with activation of primary human hepatic stellate cells, a key event during fibrogenesis, remain poorly characterized. Here, we provide the transriptomic profile underpinning the healthy phenotype of human hepatocytes, liver sinusoidal endothelial cells (LSECs) and quiescent hepatic stellate cells (qHSCs) as well as activated HSCs (aHSCs) We assess the transcriptome for purified, non-cultured human hepatocytes, liver sinusoidal cells (LSECs) and quiescent hepatic stellate cells (qHSCs) as well as culture-activated HSCs (aHSCs). Hepatocytes (n=2 donors), LSECs (n=3), qHSCs (n=3) and in vitro activated HSCs (n=3; from the same donors as the qHSCs and LSECs) were used for this study.

2016-03-02 | E-GEOD-68000 | biostudies-arrayexpress

Freshly isolated rat liver sinusoidal endothelial cells and Kupffer cells, LC-MSMS

Project description:Liver sinusoidal endothelial cells (LSECs) and Kupffer cells (KCs) have important roles in liver homeostasis and host defense. Sharing the same microenvironment in the liver sinusoid, they form an effective scavenger cell system for removal of potentially harmful blood-borne substances. Unlike most other endothelia, LSECs are highly efficient in endocytosis of nanoparticles, including virus. Though controversial, LSECs have been reported to act as antigen presenting cells, thus contributing importantly to induction of immune tolerance in liver. There are also controversies about LSEC and KC specific markers, which may be due to overlapping cell functions, species differences, and/or problems with cell purification. We therefore used label-free proteomics to characterize and quantitatively compare proteome of freshly isolated, highly pure rat LSECs (SE-1/CD32b positive) and KCs (CD11b/c positive.We found that most immune genes expressed in KCs were also expressed in LSECs, albeit at a lower density, and they also have overlap in cell surface marker expression. Both cell types express high levels of scavenger receptors and immune lectins.

2020-11-11 | PXD012080 | Pride

Expression profiling in hiPSC-derived liver sinusoidal endothelial cells and hepatic stellate cells

Project description:We have established culture systems to generate liver sinusoidal endothelial cells (LSECs) and hepatic stellate cells (HSCs) from hiPSCs. To characterize gene expression profiling in hiPSC-derived LSECs and HSCs, transcriptome analysis was performed.

2017-07-27 | GSE92771 | GEO

Genome-wide analysis of DNA methylation and gene expression patterns in purified, uncultured human liver cells and activated hepatic stellate cells

Project description:The human liver contains multiple cell types whose epigenetic patterns are undetermined. We examined the promoter methylome of purified and uncultured hepatic stellate cells (HSCs), hepatocytes (HEPs) and liver sinusoidal endothelial cells (LSECs), by methylated DNA immunoprecipitation (MeDIP) and array hybridization. Uncultured HSCs, LSECs and Heps show ~7000-8000 methylated promoters, with 60-70% similarity between all cell types. GO analysis for commonly methylated genes reveals involvement in germ cell development, segregating germ-line from somatic lineage methylation. HSCs, LSECs and HEPs also contain ~500-1000 uniquely methylated promoters; these are implicated in signaling and biosynthetic processes (HSCs), lipid transport and metabolism (LSECs), and chromatin assembly (HEPs). The promoter methylome of culture-activated HSCs deviates from that of their uncultured (quiescent) counterparts. HSC culture-induced activation also enhances methylation differences between individual donors; however this does not necessarily relate to changes in gene expression. HSc activation results in a net gain of promoter DNA methylation, despite the demethylation and de novo methylation of thousands of promoters. Our data provide to our knowledge the first genome-wide maps of promoter DNA methylation in human purified and uncultured liver cell types. Although methylation profiles are largely similar between HSCs, LSECs and hepatocytes, the detection of cell type-specific methylation patterns suggests a differential epigenetic programming of these cell types in the liver. Determine the promoter DNA methylation pattern of 3 uncultured, reshly isolated, human healthy liver cell types (hepatocytes (HEPs), liver sinusoidal endothelial cells (LSECs) and haptic stellate cells (HSCs), and of HSCs after a 24-h culture-induced activation.

2015-12-21 | E-GEOD-66796 | biostudies-arrayexpress

The Hepatocyte Proteome in Organotypic Rat Liver Models and the Influence of the Local Microenvironment

Project description:Liver models that closely mimic the in vivo microenvironment are central for understanding liver functions, capabilities, and intercellular communication processes. Whereas hepatocyte monolayers de-differentiate after only a few days in culture, constructs consisting of hepatocytes and non-parenchymal cells (NPC) separated by a polyelectrolyte multilayer (PEM) provide maintenance of hepatic phenotypes. To better understand the mechanisms and processes that underlie organotypic liver model function, hepatocyte protein abundances in the presence and absence of liver sinusoidal endothelial cells (LSECs) were compared to hepatocyte monolayers. The presence of the PEM led to increases in proteins associated with hepatocyte lipid metabolism, with mitochondrial-based β-oxidation and peroxisomal proteins found in higher abundance. It was also demonstrated that the presence of LSECs modulates levels of carboxylesterases and other phase I and phase II enzymes. These results are discussed in relation to intercellular signaling and hepatocyte function.

2017-07-06 | PXD002491 | Pride

Transcriptomic profiling of liver sinusoidal endothelial cells during chronic liver disease reveals stage-specific secretory signature

Project description:In this study RNAseq was used for studying the transcriptome profile of primary liver sinusoidal endothelial cells (LSECs) isolated from non-lesioned non-tumorous liver tissues (considered as healthy) and from cirrhotic liver explants (ethanol etiology). Results showed different transcriptomic profile between two populations of LSECs with 1374 significant deregulated genes (fold-change>1.5 and p-vale<0.05) in cirrhotic-LSECs compared with healthy-LSECs.

2021-09-24 | GSE164799 | GEO

Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models

Project description:In this study, genome-wide gene expression profiles of primary hepatocytes and liver sinusoidal endothelial cells (LSECs) were measured at day 12 for each cell culture system using Affymetrix GeneChips and analyzed via Gene Set Enrichment Analysis (GSEA). The culture systems analyzed include the commonly used collagen sandwich and monolayers of hepatocytes, as well as 3-dimensional (3D) engineered liver models that contain hepatocytes and LSECs (3DHL) and hepatocytes, LSECs, and Kupffer cells (3DHLK). Our results highlight the up-regulation of several hepatocyte specific functions in hepatocytes and a novel interplay between Ppara signaling and bile acid biosynthesis in LSECs.

2018-04-27 | GSE74424 | GEO

H3K27ac profiling in liver sinusoidal endothelial cells through chromatin immunoprecipitation and sequencing

Project description:Portal hypertension (PHTN) is a severe complication of liver cirrhosis. It is associated with intrahepatic sinusoidal remodeling induced by sinusoidal resistance and angiogenesis. Collagen type IV (COL4), a major component of basement membrane (BM), forms in liver sinusoids upon chronic liver injury. However, the cellular source and transcriptional regulation of COL4, as well as how it progresses in liver diseases is unknown. Here, we examined how COL4 is produced and how it regulates sinusoidal remodeling in PHTN. RNA-seq analysis on human cirrhotic livers revealed an increase in COL4 expression, which was further confirmed via immunofluorescence (IF) staining. scRNA-seq analysis identified Liver sinusoidal endothelial cells (LSECs) as the predominant source of COL4 expression in mouse liver, which was upregulated in a TNFα-NFκB dependent manner. Epigenetic repression of enhancer-promoter interaction silences COL4 gene expression via dCas9-KRAB-mediated epigenome editing approach. LSEC-specific COL4 mutation or repression abrogated sinusoidal resistance and angiogenesis, thereby alleviated sinusoidal remodeling and PHTN. Our findings reveal LSECs as a major source of COL4 in the liver which plays a prominent role in sinusoidal remodeling and PHTN.

2024-01-01 | GSE233284 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data