Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Age-Dependent Transcriptional Alterations in Cardiac Endothelial Cells [scRNA-seq]

ABSTRACT: Purpose: The goal of this study is to determine alterations in heart endothelial cell transcripts and cell populations associated with aging. Methods: Endothelial single cell mRNA profiles of 3 month and 24 month old wild-type mice were generated by 10X Genomics Results: Using an optimized data analysis workflow, we mapped about 50 thousand reads per cell Conclusions: Our study represents the first analysis of aged cardiac endothelial cell transcriptomes using single cell RNA-seq technology, identifiying specific transcripts and cell populations affected by age.

ORGANISM(S): Mus musculus

PROVIDER: GSE163822 | GEO | 2021/05/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Age-Dependent Transcriptional Alterations in Cardiac Endothelial Cells [bulk RNA-seq]

Project description:Purpose: The goal of this study is to determine alterations in heart endothelial cell transcripts associated with aging. This is accomplished by comparing endothelial transcriptomes from young and aged organs (heart, brain and kidney). Methods: Endothelial mRNA profiles of 3 month and 24 month old wild-type mice were generated by next generation sequencing using libraries generated via SmartSeq V4 chemistry (Takara) and sequenced on an HiSeq 2500 (Illuina). Tophat2 with default parameters was used to align the sequenced reads against the mouse genome using the GRCm38. HTSeq python software with default parameters was used to quantify the transcripts of the aligned reads using the corresponding GRCm38 gene annotation model from Ensembl. Results: Highly enriched populations of endothelial cells (ECs) isolated from the heart, brain and kidney of young (3 months) and old (24 months) C57/BL6 mice were profiled for RNA expression via bulk RNA sequencing. Approximately 700 cardiac endothelial transcripts significantly differ by age. Gene set enrichment analysis indicated similar patterns for cellular pathway perturbations. Receptor-ligand comparisons indicated parallel alterations in age-affected circulating factors and cardiac endothelial-expressed receptors. Single-cell RNA-seq analysis identified 9 distinct endothelial cell subtypes in the heart with an age-associated population shift observed for an Aplnr-enriched endothelial cell clusters. Conclusions: Gene and pathway enrichment analyses show that age-related transcriptional response of cardiac endothelial cells is distinct from that of endothelial cells derived from the brain or kidney vascular bed. Furthermore, single-cell analysis identified 9 distinct EC subtypes, and shows that Aplnr-enriched subtype is reduced with age in mouse heart. Finally, we identify age-dysregulated genes in specific aged cardiac endothelial subtypes.

2021-05-28 | GSE163821 | GEO

Single-cell transcriptomic analysis of 36 hpf Zebrafish etv2 and jam2b positive cells

Project description:We performed single-cell RNAseq analysis of FACs sorted etv2 and jam2b psoitive cells from etv2Gt(2A-Venus) ; jam2bGt(2A-Gal4);UAS:NTR-mCherry zebrafish embryos at 36 hpf using 10x Genomics' Chromium platform. 18 distinct cell populations were identified including vascular endothelial cells and LPM cells.

2021-07-13 | GSE179926 | GEO

Single cell RNA-Seq of four human kidney organoids

Project description:These files represent single cell RNA-Seq data generated on a 10x Chromium genomics platform from four biological replicates of iPSC-derived human kidney organoids, in two batches, differentiated according to our published protocol (Takasato et al., Nature Protocols 2016). The aggregated human organoid data contains populations representing endothelial cells, podocytes, stroma, nephron, and off-target populations with similarity to neurons.

2018-12-07 | GSE114802 | GEO

Transcriptional remodeling of human dermal blood vascular and lymphatic endothelial cells in psoriasis

Project description:Single-cell transcriptomic profiling of CD45-CD31+ endothelial cells derived from healthy and psoriatic human skin using the 10x Genomics platform.

2022-05-26 | E-MTAB-11218 | biostudies-arrayexpress

Single cell RNA-seq of single cell suspension from the HCC region of WT and FABP5 Hepatocyte KO mice fed CD-HFD for 15 month

Project description:After feeding CD-HFD diet for 15 month, tumors from WT and FABP5 hepatocyte KO mice were collected and digested with collagenase to generate single cell suspension before proceeding with 10X Single Cell RNA-Sequencing.

2024-02-23 | GSE248010 | GEO

single-cell RNA sequencing on Drosophila melanogaster brain in an ALS/FTD model

Project description:The mutation in the C9orf72 gene with a hexanucleotide repeat has been reported multiple times to be the most common genetic cause of FTD and ALS (Frontotemporal Dementia and Amyotrophic Lateral Sclerosis), both of which are devastating neurodegenerative diseases having no cures currently. Our lab previously created fruit fly models expressing 36(C4G2) repeats, these are highly toxic to adult neurons of fruit flies. This is one of the most commonly used fly models of disease. Like many neurodegenerative diseases, FTD and ALS display selective neuronal vulnerability: only some neuronal populations succumb to disease, even though the toxic species are ubiquitously expressed. Our lab proposes to identify which neuronal populations are selectively depleted in response to the expression of the repeats and analyse which pathways are activated in vulnerable and resistant neuronal populations using our fly model of disease. This is done by scRNA sequencing across multiple time points, tracking disease development. The workflow was first having the flies ready and their brains being dissected. The brains were then dissociated by collagenase and dispase, and the cell suspensions were passed through a 10um cell strainer. The single-cell suspensions were checked for viability and the single-cell libraries were prepared with 10X Chromium 3' platform.

2023-11-09 | E-MTAB-12440 | biostudies-arrayexpress

High-throughput error corrected Nanopore single cell transcriptome sequencing

Project description:E18 mouse brain single cell profiling using the 10x Genomics Chromium instrument workflow with either Illumina short read sequencing for the standard gene profiling and Nanopore PromethION long read sequencing for isoform profiling.

2020-07-10 | GSE130708 | GEO

Single cell transcriptional profiling of aortic endothelium identifies a hierarchy from endovascular progenitors to differentiated cells

Project description:We performed 3' single-cell RNA-seq using the 10X Genomics Chromium (version 2 chemistry) system on ~6,000 mouse endothelial cells derived from aorta.

2019-05-27 | E-MTAB-7149 | biostudies-arrayexpress

Single cell CITE-seq and VDJ sequencing of epidermal and blood T cells

Project description:The aim of the experiment was to investigate the clonal relationship between CD8+ T cell subsets of donor matched blood with epidermal CD8+ T cells. Abdominal skin (n=8) was separated into dermis and epidermis, followed by epidermal skin and PBMC isolation. Single CD8+ T cells (n=6) and CD3+ T cells (n=2) were FACS sorted, processed with the 5’ 10x Genomics workflow and sequenced at NGI Sweden.

2023-06-12 | E-MTAB-12839 | biostudies-arrayexpress

Aged blood impairs hippocampal neural precursor activity and activates microglia via brain endothelial cell VCAM1

Project description:Single cell RNAseq of Old (19 month) and Young (3 month) mouse brain endothelial cells isolated from hippocampi of C57BL6 males.

2019-03-07 | GSE127963 | 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