Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ena-DATASET-DKFZ-29-05-2020-15:56:12:496-205 - samples

ABSTRACT: ALI culture bronchial cells and alveolar lung surgical resection scRNA-Seq

PROVIDER: EGAD00001006185 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Publications

SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells.

Lukassen Soeren S Chua Robert Lorenz RL Trefzer Timo T Kahn Nicolas C NC Schneider Marc A MA Muley Thomas T Winter Hauke H Meister Michael M Veith Carmen C Boots Agnes W AW Hennig Bianca P BP Kreuter Michael M Conrad Christian C Eils Roland R

The EMBO journal 20200414 10

The SARS-CoV-2 pandemic affecting the human respiratory system severely challenges public health and urgently demands for increasing our understanding of COVID-19 pathogenesis, especially host factors facilitating virus infection and replication. SARS-CoV-2 was reported to enter cells via binding to ACE2, followed by its priming by TMPRSS2. Here, we investigate ACE2 and TMPRSS2 expression levels and their distribution across cell types in lung tissue (twelve donors, 39,778 cells) and in cells de ...[more]

PMID: 32246845

Similar Datasets

Human alveolar progenitors generate dual lineage bronchioalveolar organoids

Project description:Mechanisms of epithelial renewal in the alveolar compartment remain incompletely understood. To this end, we aimed to characterize alveolar progenitors. Single-cell RNA-seq (scRNA-seq) analysis of the HTII-280 positive and HTII-280+ /EpCAM+populations from total 6 donors from periferal tissue was performed, and analysis revealed subclusters enriched for stem cell signature genes. We found that these alveolar progenitors in organoid culture in vitro show phenotypic lineage plasticity as they can yield alveolar or bronchial cell type progeny. The direction of the differentiation is dependent on the presence of the GSK-3β inhibitor, CHIR99021. By RNA-seq analysis of GSK-3 βknockdown organoids, we identify additional functional candidate target genes and pathways which contribute to alveolar differentiation independent of Wnt signaling

2022-07-08 | GSE197949 | GEO

Single-cell sequencing highlights increased atypical AT2 interacting with M1 macrophage in COPD

Project description:We have constructed a transcriptomic map of airways using lung tissues from three COPD (GOLD grade I) who underwent surgical resection for lung cancer. We performed 5' single-cell RNA sequencing (scRNA-seq) on three COPD and three control matched lung tissue, as well as the organoid samples.

2024-06-28 | GSE270667 | GEO

The 5p12 breast cancer susceptibility locus affects MRPS30 expression in estrogen-receptor positive tumors

Project description:Uninvolved tissue taken at the time of primary surgical resection of an adenocarcinoma. Uninvolved status determined by surgical margin and gross appearance, not pathology

2014-05-22 | GSE48067 | GEO

scRNA-seq of canalicular stage human fetal lung cultured under air-liquid interface

Project description:Small pieces (<0.5 cm of diameter) were isolated from distal regions of 125 day male human fetal lung and cultured on floating poly-carbonate membranes on top of serum and growth factor free medium under air-liquid interface conditons (ALI). ALI explants underwent changes in gene expression indicative of alveolar epithelial cell differentiation under these conditions. scRNA-sequencing was performed on fetal tissue prior to culture (day 0) and day 3, 6, 9 and 12 of ALI explant culture.

2023-06-15 | E-MTAB-12959 | biostudies-arrayexpress

Gene-expression profiles of formalin-fixed, paraffin-embedded human hepatocellular carcinoma

Project description:Gene-expression profiles of formalin-fixed, paraffin-embedded human hepatocellular carcinoma tissues obtained at the time of surgical resection. Gene-expression profiling was performed using formalin-fixed, paraffin-embedded hepatocellular carcinoma tissues obtained at the time of surgical resection.

2011-02-17 | E-GEOD-19977 | biostudies-arrayexpress

Serum miRNA in liver disease

Project description:Aiming to develop novel biomarker for cancer prediction after surgical resection In title X-Y: X represents a patient number. Y represents the order in which the blood was collected during surgical treatment.

2016-12-31 | GSE85679 | GEO

Cellular response to hypoxia on human bronchial epithelial culture [scRNA-Seq]

Project description:Cellular response to hypoxia on human bronchial epithelial culture [scRNA-Seq]

| PRJNA945417 | ENA

Exposure to aerosol of an e-vapor device with MESH™ technology had a lower biological impact than exposure to cigarette smoke on human bronchial and alveolar culture models: an in vitro systems toxicology assessment.

Project description:The harmful effects of cigarette smoke exposure on the respiratory tract are widely known. Exposure to aerosol from electronic vapor (e-vapor) products has been suggested to result in less risk of harm to smokers than CS exposure. Many studies have assessed the potential toxicity of the aerosol from e-vapor products in vitro. However, most studies have only tested the effects of liquid formulations applied directly to cell cultures but not those of the aerosolized formulations. In this study, we examined the effects of acute exposure on human organotypic bronchial epithelial culture and alveolar tri-culture models to an aerosol generated by an e-vapor device that uses the MESH™ technology (IQOS® MESH, Philip Morris International) and to CS from the 3R4F reference cigarette. In contrast to 3R4F CS exposure, exposure to the IQOS MESH Classic Tobacco aerosol did not cause cytotoxicity in either of the two lung culture models, despite resulting in greater concentrations of deposited nicotine. Ciliary beating frequency in bronchial cultures was not impacted in response to IQOS MESH aerosol exposure, whereas CS exposure caused a marked decrease in the frequency and the cilia beating active area. We complemented the histological and functional findings with quantitative analysis of the molecular changes in the exposed cultures. Global mRNA expression profiles and secreted protein profiles revealed a significantly lower impact of exposure to IQOS MESH aerosol than to 3R4F CS exposure. Overall, our study using whole aerosols for the exposure shows a much reduced impact of IQOS MESH aerosol in comparison to CS exposure in both bronchial and alveolar cultures, even at greater nicotine doses.

2021-01-31 | E-MTAB-10071 | biostudies-arrayexpress

Gene-expression profiles of formalin-fixed, paraffin-embedded human hepatocellular carcinoma

Project description:Gene-expression profiles of formalin-fixed, paraffin-embedded human hepatocellular carcinoma tissues obtained at the time of surgical resection.

2011-02-17 | GSE19977 | GEO

Comparative Tissue Proteomics for the Diagnosis of Indeterminate Pulmonary Nodules

Project description:We identified candidate protein biomarkers to distinguish lung adenocarcinomas from benign nodules. We employed shotgun proteomics using a multidimensional peptide separation approach coupled to tandem mass spectrometry (LC-MS/MS) to characterize proteomes of a collection of 34 benign lung nodules. The benign lung nodule inventories were compared to inventories from early stage lung adenocarcinomas, from 24 patients with non-adjuvant treatment following the resection, and to inventories from normal tissue collected from 10 patients as bronchial and alveolar epithelium to identify biomarkers.We developed PRM assays to quantify a subset of 43 candidate biomarker proteins via 170 tryptic peptides in a single LC-PRM-MS run using a validation cohort of 20 benign nodules, 20 adenocarcinoma, and 20 normal lung tissues.

2016-10-09 | MSV000080236 | MassIVE

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