Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq analysis of bone marrow endothelial cells

ABSTRACT: Although endothelial cells (ECs) have been shown to contribute to HSC maintenance in bone marrow (BM), differential contributions of EC subtypes remain unknown, owing to the lack of methods to separate with high purity arterial (AEC) from sinusoidal (SEC) endothelial cells. We show that combination of podoplanin (PDPN) and Sca-1 expression distinguishes AEC from SEC where Sca1brightPDPN—CD45—Ter119— cells exhibit an arterial gene signature and PDPN+Sca1dimCD45—Ter119— marks sinusoids. PDPN can be substituted for antibodies against the adhesion molecules ICAM1 or E-selectin that also mark SEC. We performed functional analysis of these different types of endothelial cells and found that SCF secreated from AECs regulate HSCs.

ORGANISM(S): Mus musculus

PROVIDER: GSE104701 | GEO | 2018/06/27

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Single-cell transcriptome Atlas reveals embryonic endothelial heterogeneity

Project description:Mature endothelial cells (ECs) are heterogeneous, with subtypes defined by tissue origin and by position within the vascular bed. Here, we performed scRNA-seq with mouse embryonic ECs and identified 19 subclusters, including Etv2+Bnip3+ early EC progenitors. Most of these subtypes were grouped by their vascular-bed types, while ECs from brain, heart and liver were grouped by their tissue origins. Compared to arterial ECs (aECs), embryonic venous (vECs) and capillary ECs (cECs) shared less markers with their adult counterparts. cECs showed some venous characteristics. One cEC cluster with both venous and capillary features served as a branch point for aEC and vEC lineages. aECs and vECs showed distinct transcriptional regulatory networks.

2024-01-25 | GSE216970 | GEO

Effects of an In Vivo Vaping Challenge on In Vitro IL-6 Biosynthesis Pathways in Arterial Endothelial Cells Derived from Human Embryonic Stem Cells

Project description:Electronic nicotine delivery system (ENDs) use among youth and young adults is increasing at a rapid pace and represents a growing public health threat.1 Newer generation devices heat e-liquids to higher temperatures and can achieve higher serum nicotine concentrations than older devices.1 Interleukin-6 (IL-6) is a cytokine that mediates atherogenesis and independently predicts future atherosclerotic cardiovascular disease events.2 Previous in vitro studies have demonstrated increased IL-6 production by human alveolar macrophages exposed to ENDs condensate.3 Although there has been considerable focus on the effects of ENDs use on airway inflammation, there are a paucity of data on the effects of ENDS on arterial inflammation. Prior in vitro studies used venous endothelial cells (VECs) or human umbilical VECs as a proxy for arterial endothelial cells (AECs), limiting generalizability of their findings. Historically, use of AECs was limited by the invasive collection methods. We used a novel in vitro AEC model of human embryonic stem-cell-derived AECs to study differential expression (DE) of IL-6 pathway genes after exposure to serum from human participants taken before and after vaping using 3rd or 4th generation ENDs or no product use.

2024-06-05 | GSE234205 | GEO

Gene expression data of nasopharyngeal carcinoma (NPC) cell and Podoplanin (PDPN) siRNA treatment

Project description:Podoplanin, a transmembrane sialomucin-like glycoprotein, is now widely used as a marker for lymphatic endothelial cells and fibroblastic reticular cells in lymphoid organs, but its study in nasopharyngeal carcinoma (NPC) is still limited. The aims of this study were t characterize the role of PDPN in NPC. Our results showed that PDPN was expressed in most TW01 NPC cells. PDPN knockdown by siRNA decreased NPC cell proliferation, migration, and invasion. Knocking down PDPN results in suppression of NPC cell proliferation, migration, and invasion. PDPN may serve as a potential chemotherapeutic target for NPC treatment in the future.

2019-03-19 | GSE128502 | GEO

Gene expression of RAW264.7 with or without Pdpn expression before and after H. pylori infection

Project description:The effect of Podoplanin (Pdpn) expression on the differential expression profile of RAW264.7 cells has been characterised in wildtype, Pdpn knockout cells and Pdpn overexpressed cells before and after H. pylori infection using 770 genes from the NanoString Mouse PanCancer Pathways Panel.

2020-05-28 | GSE151269 | GEO

Human arterial endothelial cells from pluripotent stem cells for in vitro hematopoiesis and lymphopoiesis

Project description:Arterial endothelial cells (AECs) are the founder cell for intraembryonic haematopoiesis. Here, we report a method for the efficient generation of human haemogenic DLL4+ AECs from pluripotent stem cells (PSC). Time-series single cell RNA-sequencing revealed the dynamic evolution of haematopoiesis and lymphopoiesis from endothelial stage, generating cell types with counterparts present in early human embryos. Our study describes an efficient method for producing lymphoid cells and provides insights into their endothelial and haematopoietic ontogeny, paving a new path to investigations of the human blood system.

2024-08-01 | GSE217705 | GEO

DNA Methylation Profiles of Airway Epithelial Cells and PBMCs from Healthy, Atopic and Asthmatic Children.

Project description:DNA methylation profiling of airway epithelial cells (AECs) and peripheral blood mononuclear cells (PBMCs) from normal, atopic and asthmatic subjects. The Illumina GoldenGate Methylation Cancer Panel I was used to obtain DNA methylation profiles across approximately 1505 CpGs in AECs and PBMCs. Samples included 7 healthy, 9 atopic, 4 atopic asthmatic and 5 non-atopic asthmatic subjects. Please note that only some of the samples are matched (i.e. AECs and PBMCs from the same individual) due to DNA quality or sample collection (i.e. only one sample (AEC or PBMC) was collected from the patient). Bisulphite converted DNA from the 41 samples were hybridised to the Illumina GoldenGate Methylation Beadchip

2012-05-08 | E-GEOD-37853 | biostudies-arrayexpress

Gene expression analysis of airway epithelial cells exposed to flagellin via RNA-seq

Project description:Airway epithelial cells (AEC) are critical components of the inflammatory and immune response during exposure to pathogens. AECs in monolayer culture and differentiated epithelial cells in air-liquid interface (ALI) represent two distinct and commonly used in vitro models, yet differences in their response to pathogens have not been investigated. In this study, we compared the transcriptional effects of flagellin on AECs in monolayer culture versus ALI culture using exon microarrays and RNAsequencing. We found that AECs cultured in monolayer and ALI have strikingly different transcriptional states at baseline. When challenged with flagellin, monolayer AEC cultures greatly increased transcription of numerous genes mapping to wounding response, immunity and inflammatory response. In contrast, AECs in ALI culture had an unexpectedly muted response to flagellin, both in number of genes expressed and relative enrichment of inflammatory and immune pathways. In conclusion, In vitro culturing methods have a dramatic effect on the transcriptional profile of AECs at baseline and after stimulation with flagellin. These differences suggest that epithelial responses to pathogen challenges are distinctly different in culture models of intact and injured epithelium.

2014-12-01 | GSE55458 | GEO

Gene expression analysis of airway epithelial cells exposed to flagellin via microarray

2014-12-01 | GSE55459 | GEO

Expression data from developing mouse livers

Project description:Roles of mesothelial cells (MCs) are poorly understood during liver development and injury. We identified podoplanin (Pdpn) as a cell surface markers for mesothelial cells in E12.5 mouse developing liver. To identify genes uniquely expressed in MCs, we isolated MCs from E12.5 mouse livers by FACS using anti-Pdpn antibodies and performed microarray analysis. The E12.5 liver was digested with trypsin-EDTA and incubated with antibodies against Pdpn. MCs were isolated as Pdpn+ population by FACS. Total RNA was extracted with RNAqueous Micro (Ambion) and the probes for the microarray were synthesized using the Ovation RNA amplification system V2 and FL-Ovation cDNA Biotin module V2 (Nugen). The labeled probes were hybridized with GeneChip Mouse Genome 430 2.0 arrays (Affymetrix) and signals were analyzed with Genomic Suite software (Partek).

2013-02-04 | E-GEOD-39064 | biostudies-arrayexpress

AEC II cell differentiation in miR142 overexpressing mice

Project description:We observed that loss of miR142 leads to the increased expression of surfactant protein C and decreased Podoplanin. This indicates increased differentiation of alveolar progenitors towards AEC II lineage. In order to understand what are the genes that are being regulated during AEC II cell differentiation in miR142 overexpressing mice we are performing this experiment.

2019-11-01 | GSE106410 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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