Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Joint single-cell/single-nucleus RNA-seq on hearts from healthy or HFpEF mice

ABSTRACT: In this project we explore the cellular heterogeneity of a mouse model of heart failure with preserved ejection fraction (HFpEF) involving a two-hit model of feeding a high fat diet (HFD) along with L-NAME administration. Healthy adult male mice (C57BL/6J inbred) were fed either a normal chow diet or HFD/L-NAME for 10 weeks or 15 weeks before performing sequencing experiments. Both cardiomyocytes (CMs) and total interstitial population (TIP) were captured using a protocol to jointly capture and sequence single-nuclei (for cardiomyocytes) and single-cells (for TIP) using the 10x Genomics Chromium system.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Ralph Patrick

PROVIDER: E-MTAB-13362 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single cell sequencing analysis of senescence in Mus musculus prostate cancer models

Project description:Acute Pten loss initiates prostate tumorigenesis characterized by cellular senescence response. Here we examine the cellular senescence response in epithelial individual cells, by single-cell RNA sequencing (scRNAseq) in Ptenpc-/- and Ptenpc-/-; Timp1-/- GEMMs. ScRNAseq analysis determines a cluster of senescent cells expressing the senescence-related genes. A significant positive correlation is observed between the senescence score and Bcl2 expression. This provides the rational for targeting senescent cells using Bcl2 inhibitor.

2020-10-09 | E-MTAB-9578 | biostudies-arrayexpress

Human embryonic yolk sac CITE-seq data

Project description:In this study we used single cell multi-omics profiling to create an atlas of the human YS to gain insights into its haematopoietic, metabolic and nutritive functions during early embryonic development. This contains CITE-seq data (surface protein and cytosolic RNA content) data from two biological replicates. Pooled lanes were demultiplexed using SoupOrCell (for alignment and demultiplexing software and version numbers, please see accompanying manuscript and protocols within this accession). Raw count files provided are directly as output by alignment software, without any quality control applied. Quality control is described in accompanying manuscript methods. Metadata by barcode are provided as supplementary tables in accompanying manuscript.

2022-12-08 | E-MTAB-11549 | biostudies-arrayexpress

Single nucleus RNA sequencing of human iPSC-derived forebrain organoids to assay cell type composition

Project description:Human iPSC line D1 was differentiated into spheroids. After 21 weeks in culture, single nucei were extracted and assayed using single nucleus RNA sequencing to characterize the spheroids' cell type composition.

2021-12-01 | E-MTAB-10605 | biostudies-arrayexpress

scRNA-seq of Human Alveolar Type 2 Cell Organoids

Project description:Alveolar type 2 (AT2) cells function as stem cells in the adult lung and aid in injury-repair. The current study aimed to understand the signaling events that control differentiation of this therapeutically relevant cell type during human development through differentiation of lung progenitor organoids to AT2 cells and benchmarking against primary AT2 organoids.

2023-06-15 | E-MTAB-12960 | biostudies-arrayexpress

Single-cell RNA-seq (10x Chromium V3) of zebrafish csf1ra and csf1rb mutant whole kidney marrows

Project description:Macrophage colony-stimulating factor receptor (M-CSFR/CSF1R) signaling is crucial for the differentiation, proliferation, and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases, including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore, it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human-related diseases. Here, we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single-cell RNA sequencing. Our analysis of adult whole kidney marrow (WKM) hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non-overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease, mostly in cancerogenesis.

2021-04-24 | E-MTAB-10360 | biostudies-arrayexpress

Single-cell RNA-seq of fibroblasts influenced by exosomes derived from melanoma cell line G361

Project description:In this in-vitro study, we demonstrated the different effects of exosomes produced by G361 melanoma cells on the functional properties of normal dermal fibroblasts and fibroblasts prepared from skin metastasis of cutaneous malignant melanoma. Both normal and cancer-associated fibroblasts were cultivated in either DMEM with 10% EDS (exosome-depleted serum) (control) or DMEM with 10% EDS + 10 microg/ml G361 exosomes (EXO). The cells were harvested after 24 hours of cultivation.

2021-12-31 | E-MTAB-10290 | biostudies-arrayexpress

Age-dependent RGS5 loss in pericytes induces cardiac dysfunction and fibrosis in the heart

Project description:Background. Ageing is one of the main risk factors of cardiovascular disease. Pericytes are capillary-associated mural cells involved in the maintenance and stability of the vascular network. In the heart, the consequences of ageing on cardiac pericytes are unknown. Methods. In this study, we have combined single nucleus RNA sequencing and histological analysis to determine the effects of ageing on cardiac pericytes. Furthermore, we have conducted in vivo and in vitro analysis of RGS5 loss of function and finally have perfomed pericytes-fibroblasts co-culture studies to understand the effect of RGS5 loss of function in pericytes on the neighbouring fibroblasts. Results. We showed that ageing reduces the pericyte area and coverage. Single nucleus RNA sequencing analysis further revealed that the expression of the Regulator of G protein signalling 5 (Rgs5) is reduced in old cardiac pericytes. In vivo and in vitro studies showed that the deletion of RGS5 induces morphological changes and a pro-fibrotic gene expression signature characterized by the expression of different extracellular matrix components and growth factors like TGFB2 and PDGFB in pericytes. Indeed, the culture of fibroblasts with the supernatant of RGS5 deficient pericytes induced their activation characterized by the increased expression of α smooth muscle actin in a TFGβ2 dependent mechanism. Conclusions. Our results identify RGS5 as a crucial regulator of pericyte function during cardiac ageing. The deletion of RGS5 causes cardiac dysfunction and induces myocardial fibrosis, one of the hallmarks of cardiac ageing.

2024-03-06 | E-MTAB-13841 | biostudies-arrayexpress

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

Iron accumulation drives fibrosis, senescence, and the senescence-associated secretory phenotype

Project description:We found histological evidence for increased abundance of iron accumulating cells in association with fibrotic lung, kidney, and heart diseases in mice and humans. We showed that inducing iron accumulation by intratracheal iron delivery in mice is a potent inducer of inflammation, cellular senescence, and fibrosis. The aim of this study has been to understand the single cell dynamics of iron accumulation and the mechanics that link it to in vivo senescence and to fibrogenesis. To get deeper insight into how different cell types respond to iron accumulation, we performed single nuclei RNA sequencing (snRNA-seq) of lungs from mice which received a single intratracheal dose of iron 2 or 6 days prior to analysis, or PBS 6days prior to analysis (control).

2023-08-18 | E-MTAB-13032 | biostudies-arrayexpress

Single-cell RNA-seq of mouse cardiac interstitial cells 3 & 7 days after sham or myocardial infarction injury and PDGF-AB or PBS delivery

Project description:The aims of the experiment were to profile the cardiac interstitial (non-myocyte) cell types in the adult mouse from injured and uninjured hearts and how they respond to modulation of platelet-derived growth factor receptor alpha (PDGFRa) signaling. Adult, male, C57BL/BJ mice were subject to either a myocardial infarction or sham injury, and given either PDGF-AB or PBS treatment via mini-pump, with single-cell RNA-seq profiles obtained from interstitial cells isolated from cardiac ventricles 3 or 7 days following surgery.

2023-05-31 | E-MTAB-7971 | 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