Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Clonal hematopoiesis activates pro-calcific pathways in macrophages and promotes aortic valve stenosis

ABSTRACT: PBMCs of patients with AVS having TET2 mutations versus those with no known CHIP mutations were utilized for scRNA-seq

INSTRUMENT(S): Illumina NovaSeq 6000, Chromium Controller, Chromium Controller / Agilent Bioanalyzer, None

ORGANISM(S): Homo sapiens

SUBMITTER: Wesley Abplanalp

PROVIDER: E-MTAB-15820 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

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

scRNAseq of immune cells of patients with chronic graft-versus-host disease

Project description:In this study, we investigated somatic mutations in T cells in patients with various hematological disorders. To analyze immune cell phenotypes with somatic mutations, we performed scRNA+TCRab sequencing from 9 patients with chronic GVHD and clonal expansions of CD4+ or CD8+ T cells based on T cell receptor sequencing. CD45+ PBMCs (lymphocytes and monocytes) were sorted with BD Influx cell sorter and subjected to sequencing with Chromium VDJ and Gene Expression platform (v1.1, 10X Genomics). Sequencing was performed with Novaseq 6000 (Illumina). The immune cell phenotypes were compared to healthy controls processed in the same laboratory (accession number E-MTAB-11170). Due to data privacy concerns, the raw sequencing data is in the European Genome-Phenome Archive (EGA) under accession code [xxxx] and can be requested through the EGA Data Access Committee.

2024-04-10 | E-MTAB-13419 | biostudies-arrayexpress

scRNA-seq data for Distinct Stem Cell Identities Converge into Shared Erythroid Stress in ERCC6L2 Disease and Shwachman-Diamond Syndrome

Project description:This study includes single-cell RNA sequencing of human samples across ERCC6L2 disease (ED), Shwachman-Diamond syndrome (SDS), acute myeloid leukemia (AML), and healthy controls. ED, SDS, and AML samples were processed for single-cell capture, followed by library preparation and sequencing. Sequencing reads were processed through standard pipelines, including quality control, alignment, and quantification, to generate expression matrices. The dataset contains processed single-cell gene expression data, and curated metadata describing sample identity, cell populations, and disease classification. Related raw sequencing files will be available at FEGA.

2026-06-03 | E-MTAB-16984 | 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

Single cell RNA-seq to resolve heterogeneity in a cardiac differentiation timecourse

Project description:Differentiation of HES3 hESCs using BMP4, Activin A and CHIR99021. 5 timepoints of sample collection (day 3-12). Differentiations were started sequentially and collected and processed on the same day. Sample1 = day 3 + day3.75 (50:50 mix); Sample2 = day 4.75; Sample3 = day 5.75; Sample 4 = day 12.

2025-01-31 | E-MTAB-14249 | 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

Charting the age-altered thymic epithelial cell differentiation by lineage tracing from a beta 5-t expressing TEC progenitor

Project description:TEC progenitors that express beta 5-t contribute to both the cortical and medullary TEC compartments. Our initial experiments across ageing thymi identified a population of potential progenitor TECs which expanded with age, and appears to be a progenitor population for mTEC. These lineage tracing experiments are designed to chart the altered differentiation and senescence of mTEC progenitors with age.

2020-09-14 | E-MTAB-8737 | biostudies-arrayexpress

Single cell RNAseq of uterine myeloid and CD45- cells in the steady state

Project description:The aim of this experiment was to identify specific subsets of monocytes, dendritic cells, macrophages and structural cells including epithelial cells, endothelial cells and stromal cells in the murine uterus, across all reproductive cycle stages via single cell RNA sequencing. Samples were FACS-enriched separately for populations of CD45+Ly6G-SiglecF-CD3-CD5-CD19-CD20- cells expressing MHC class II and/or CD11b (myeloid) and CD45- structural cells.

2026-08-07 | E-MTAB-15391 | biostudies-arrayexpress

Single-cell RNA sequencing analysis of left atrial appendage tissue following magnetogel-based occlusion in a porcine model

Project description:This study aims to evaluate the long-term biocompatibility and tissue integration of a novel magnetogel-based left atrial appendage (LAA) occluder. To assess the host tissue response, single-cell RNA sequencing (scRNA-seq) was performed on LAA tissue samples obtained from a preclinical porcine model after 10 months of magnetogel implantation. Tissue samples were collected from regions in direct contact with the magnetogel (contact zone) and adjacent non-contact areas. scRNA-seq analysis revealed the cellular composition, which included myofibroblasts, fibroblasts, neutrophil cells, macrophages, T cells, mast cells, smooth muscle cells, and Schwann cells. Critically, no significant differences in the ratios of immune cells (e.g., neutrophils, macrophages, T cells) or mast cells (indicative of allergic reactions) were observed between the contact and non-contact zones.

2025-12-07 | E-MTAB-15847 | biostudies-arrayexpress

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