Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of pro-fibrotic macrophages populations by scRNA-seq in West Highland white terriers affected with canine idiopathic pulmonary fibrosis

ABSTRACT: We used the scRNA-seq to characterize disease-related heterogeneity within cell populations of macrophages/monocytes in the bronchoalveolar lavage fluid from West Highland white terriers either healthy or affected with canine idioapthic pulmonary fibrosis. The disease is still not well understood, occurs in old West Highland white terriers and results from deposition of fibrotic tissue in the lung parenchyma causing respiratory failure.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Canis lupus familiaris

SUBMITTER: Aline Fastrès

PROVIDER: E-MTAB-9623 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

scRNA-seq analysis of cell subpopulations of the bronchoalveolar lavage fluid of healthy dogs

Project description:In dogs, a species for which markers of cell populations are often limiting, we sought to evaluate in an unbiased way the heterogeneity of cell subpopulations in the bronchoalveolar lavage fluid of healthy dogs, by single-cell RNA-sequencing.

2020-06-29 | E-MTAB-9265 | biostudies-arrayexpress

Clonally expanded EOMES+ Tr1-like cells in primary and metastatic tumors associate with disease progression

Project description:We performed single-cell transcriptome analysis with the 10X Genomic Chromium platform of CD4+ T cells infiltrating human primary and metastatic colorectal cancer (CRC) and non-small-cell lung cancer (NSCLC). Datasets derive from fresh samples collected and immediately processed by cell sorting and single-cell isolation 10X protocol. A total number of 10000 cells per sample was analyzed by scRNA-seq.

2021-04-28 | E-MTAB-7006 | biostudies-arrayexpress

scRNA-seq analysis of lung neutrophils from mice, 24 hours after intranasal exposure to vehicle, 100 ng LPS and 10 µg LPS

Project description:Mice intranasally exposed to a low dose of LPS (i.e., 100 ng) are prone to develop features of allergic asthma upon subsequent exposure to house dust mites (HDM) allergens, while mice exposed to vehicle or 100 µg LPS do not develop such features. In order to understand the mechanisms that promote allergic asthma, we sought to characterize the lung neutrophils, which are massively recruited after LPS exposure, by single cell RNA-Seq.

2019-07-25 | E-MTAB-6902 | biostudies-arrayexpress

scRNA-seq analysis of lung CD64-expressing mononuclear cells, patrolling and classical monocytes from steady-state C57BL/6J mice

Project description:We sought to evaluate in an unbiased way the heterogeneity of lung interstitial macrophages and their relationship with alveolar macrophages, lung Ly-6Chi classical monocytes and Ly-6Clo patrolling monocytes, by single cell RNA-Seq.

2019-07-31 | E-MTAB-7678 | biostudies-arrayexpress

Single cell RNA sequencing of iPSC and Human dermal fibroblasts

Project description:single cell RNA sequencing of iPSC and Human dermal fibroblasts using 10x Genomics with 3-prime, 5-prime poly(dT) primer, and 5-prime random primer. For comparison in gene, ncRNA and enhancer detection.

2021-05-13 | E-MTAB-10385 | biostudies-arrayexpress

Coupled single-cell RNA, TCR, and barcoded pMHC multimer sequencing, from virus-specific PBMC T-cells

Project description:Virus-specific CD8 T cells from PBMCs of healthy donors and hepatitis patients were enriched for recognition of a panel of feature barcode-labeled pMHC multimers. The phenotypic description was made using gene expression and TCRseq. Samples were pooled and sequenced on the same 10x Genomics sequencing chip and deconvoluted using ADT HashTag antibodies,

2024-05-01 | E-MTAB-13758 | biostudies-arrayexpress

scRNA-seq in 79 fibroblast cell lines and 31 reprogrammed induced pluripotent stem cell lines for sceQTL analysis

Project description:Here, we performed scRNA-seq on 64,018 fibroblasts from 79 donors and mapped expression quantitative trait loci (eQTLs) at the level of individual cell types. We demonstrate that the majority of eQTLs detected in fibroblasts are specific to an individual cell subtype. To address if the allelic effects on gene expression are maintained following cell reprogramming, we generated scRNA-seq data in 19,967 iPSCs from 31 reprogramed donor lines. We again identify highly cell type specific eQTLs in iPSCs, and show that that the eQTLs in fibroblasts almost entirely disappear during reprogramming.

2021-02-22 | E-MTAB-10060 | biostudies-arrayexpress

Identification of cell-intrinsic effects of clonal hematopoiesis in heart failure

Project description:Clonal hematopoiesis of indeterminate potential (CHIP) is caused by somatic mutations in hematopoietic stem cells and is associated with worse prognosis in heart failure patients. Patients harboring CHIP mutations show enhanced inflammation. However, whether these signatures are derived from the relatively low number of cells harboring mutations or are indicators of a systemic pro-inflammatory activation that is associated with CHIP is unclear. In this study, we assessed the cell-intrinsic effects of CHIP mutant-carrying cells in patients with heart failure. Using an improved protocol to detect mutant cells on a single cell level (MutDetect-Seq), we show that DNMT3A mutant monocytes exhibit altered gene expression profiles associated with inflammation and phagolysosome function. Gene expression was also significantly altered in DNMT3A mutant CD4+ T cells and NK cells, but not CD8 T cells. DNMT3A silenced CD4+ T cells and NK cells showed increased effector functions. Moreover, increased paracrine signaling pathways are predicted and validated between mutated and wild monocytes and T cells, which amplify inflammatory circuits. Taken together, these data provide novel insights into how CHIP might promote worse prognosis in heart failure patients.

2023-06-15 | E-MTAB-13016 | biostudies-arrayexpress

Data expression in alveolar macrophages induced by lipopolysaccharide in humans

Project description:Rationale: Lipopolysaccharide (LPS) is ubiquitous in the environment. Inhalation of LPS has been implicated in the pathogenesis and/or severity of several lung diseases, including pneumonia, chronic obstructive pulmonary disease and asthma. Alveolar macrophages are the main resident leukocytes exposed to inhaled antigens. Objectives: To obtain insight into which innate immune pathways become activated within human alveolar macrophages upon exposure to LPS in vivo. In seven healthy humans sterile saline was instilled into a lung segment by bronchoscope, followed by instillation of LPS into the contralateral lung. Six hours later a bilateral bronchoalveolar lavage was performed and whole-genome transcriptional profiling was done (Affymetrix HG-U133 Plus 2.0) on purified alveolar macrophages, comparing cells exposed to saline or LPS from the same individuals.

2012-09-15 | E-GEOD-40885 | biostudies-arrayexpress

Single-cell RNA-Sequencing of testis tissue from 3 mouse species and their immediate crosses

Project description:We performed an inter-species comparison of murine spermatogenesis using the inbred strains C57B6J, CAST/EiJ and CAROLI/EiJ to investigate the cell type-specific evolution of gene expression levels among closely related species. We also used F1 crosses of C57B6J and CAST/EiJ to investigate context-specific regulatory effects on gene expression in cis and trans by measuring allele-specific expression (Goncalves et al. 2012; Wittkopp et al. 2021). To this end, single-cell RNA-Sequencing data was generated from dissociated testicular tissue in each mouse strain using the 10x Genomics scRNA-Seq platform.

2023-12-11 | E-MTAB-11602 | biostudies-arrayexpress

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