Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

65 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-Cell RNA-Sequencing Reveals Placental Response under Environmental Stress

ABSTRACT: This repository provides scRNA-seq data corresponding to the manuscript \\"Single-Cell RNA-Sequencing Reveals Placental Response under Environmental Stress\\" by Van Buren, Azzara, Rangel-Moreno, de la Luz Garcia-Hernandez, Murphy, Cohen, Lin, and Park. The repository includes both count by gene matrices output from CellRanger version 6.0.1 (file names *_filtered_feature_matrix.h5 for each of the eight samples Control_1_M, Control_1_F, Control_2_M, Control_2_F, As_1_M, As_1_F, As_2_M, As_2_F), and a finalized Seurat object including cell type assignments as used for analyses in the manuscript (file name final_Seurat_obj.RData). Accompanying code used in analysis can be found at https://github.com/edvanburen/placenta_code.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Eric Van Buren

PROVIDER: E-MTAB-14214 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

Single-cell RNA-sequencing of cells from spinal cord central canal region of young adult and aged mice

Project description:The spinal cord neural stem cell potential is contained within the ependymal cells lining the central canal. This neural stem cell potential is known to decline with age in the mouse. Here, we microdissected and dissociated into single cells the central canal region from the spinal cord of 4 young adult (3-to-4-month old) and 4 aged (18-to-19-month old) C57BL/6J mice to profile the transcriptomes of cells in and around the central canal using 10x Genomics technology.

2022-12-13 | E-MTAB-11561 | biostudies-arrayexpress

Multiome RNA+ATAC on human PBMCs (snRNA-seq data)

Project description:We generated Multiome RNA+ATAC data from the same cell from human PBMC. This served as a gold benchmark for a novel integration method for multi-omics data that we developed.

2021-12-02 | E-MTAB-11225 | biostudies-arrayexpress

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

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

Project description: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.

2020-12-02 | E-MTAB-9623 | 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

scRNAseq of four syngeneic human melanoma cell lines (two replicate per cell line) to study mechanisms of resistance to the BRAF inhibitor vemurafenib

Project description:Three cell lines were derived from the A375 human melanoma (harbouring the BRAF v600e mutation; ATCC) after treatment with vemurafenib during a period of 4-5 weeks in the absence (MAPKi-resist Rep1/Rep2) or presence of the fatty acid oxidation inhibitors etomoxir (Etomoxir Rep1/Rep2) or ranolazine (Ranolazine Rep1/Rep2).

2023-06-20 | E-MTAB-12412 | biostudies-arrayexpress

Intergenic risk variant rs56258221 skews the fate of naive CD4+ T cells via miR4464-BACH2 interplay in primary sclerosing cholangitis

Project description:We correlated comprehensive T cell phenotyping data from peripheral blood to the corresponding genotype of different disease-associated and T cell related SNPs. This revealed significantly increased frequencies of naive CD4+ T cells (CD4+ TN) and T helper 17 (TH17) cells in carriers of intergenic SNP rs56258221 (BACH2/MIR4464) as compared to non-carriers. Functional experiments identified CD4+ TN from SNP-carriers to rather polarize towards pro-inflammatory subsets than into regulatory T cells (TREG). *** Due to data privacy concerns fastq files have not been uploaded ***

2024-04-22 | E-MTAB-14013 | 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

Mass Spectrometry Imaging and ScRNA-seq Techniques to Explore the Biosynthetic pathways of Bufadienolides

Project description:Bufotoxin is an endogenous toxin made up of several physiologically active components that toads deploy as a defense against their natural enemies. Bufadienolides (BDS), which is isolated from bufotoxin, is an important anticancer drug, and other components such as bufotenine and alkaloids are also important drug resources. The distribution characteristics and biosynthesis of bufotoxins in the postauricular glands (PGs) of toads are not well understood. We examined the toad's PGs using the MADLI/MSI technique, a total of 1,872 components were found, and some pharmacological components were visible. These findings indicate that bufotoxins are primarily abundant in the plasma glands (pG) and epidermal tissues of the glands. By using single-cell sequencing, it was possible to create a single-cell atlas of 9316 PGs cells. These cells were then categorized into nine clusters using marker genes, and two types of epithelial cells were verified using in situ hybridization investigations. It was confirmed that cholesterol is a precursor component of BDS biosynthesis, we concentrated on the cholesterol metabolism component and postulated the primary bile acid pathway as a downstream biosynthesis pathway of BDS through transcriptomic studies of two pG and mucous glands (MG) with distinct secretory functions. Optimal and silenced genes for potential BDS synthesis pathways, toad toxin tryptamine and alkaloid biosynthesis, terpene skeleton and steroid hormones were identified by calculating the cellular coverage of genes. Our data demonstrate the metabolic mapping of bufotoxins in the PGs of the toad, and create the first single-cell atlas of PGs in the toad, providing a reference for the study of biosynthesis of natural active ingredients in animals.

2024-11-05 | PXD057113 | Pride

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