{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Diana Sharysh"],"organism":["Sus scrofa"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15464"],"description":["The single-cell RNA-seq experiment aims to explore the cell-type composition of right coronary artery plaques to provide an overview of human-like atherosclerosis. The PCSK9 transgenic minipigs were subjected to 15 months of HFHC diet (HFHC group f, n=4; m, n=1). At the time of euthanasia, plaque parts without media were quickly processed and analyzed by scRNA-sequencing."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Animals were euthanized, and the right coronary arteries were quickly isolated and opened. The atherosclerotic plaques were dissected without media. Approximately 200-250 mg of plaque was selected, washed in HBSS, and minced. It was incubated for 60 minutes at 37 °C in 1 ml of an enzyme solution containing 1,5 mg/ml (8 U/ml) of elastase (LS002279, Worthington Biochemical), 2 mg/ml of liberase (05401119001, Sigma Aldrich) and 300 µg/ml of DNaseI (Sigma Aldrich, DN25). Non-digested tissue was disaggregated using a smooth-tipped Pasteur pipette. Reactions were stopped by adding PBS containing 0.5% bovine serum albumin (BSA). The suspension was passed through a 70 µm pore filter to remove aggregates. Cells were collected by centrifugation and resuspended in 500 µl PBS+0.5% BSA. DAPI (final concentration, 1 µg/ml final ) and Draq5 (Thermo Scientific 65-0880-96; final concentration, 5 µM) were added to enable detection of viable and dead cells. Viable cells (Draq5 positive and DAPI negative) were sorted with a FACSAria Cell Sorter.","Library Construction - After reverse transcription and cDNA amplification, sequencing libraries were prepared using the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics).","Sequencing - Libraries were sequenced in paired-end reads using a HiSeq 4000 system (Illumina) and processed with RTA v1.18.66.3.","Growth Protocol - Atherosclerosis was induced in PCSK9D374Y transgenic minipigs by feeding a standard pig feed supplemented with 20% w/w lard, 1.5% w/w cholesterol (HFHC), 0.7% NaCl w/w, from 3 until 18 months of age.","Nucleic Acid Extraction - Up to 16500 cells were loaded into each port of a Chromium Next GEM Chip G (10x Genomics)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Filtration and clusterization of cell barcodes were performed using Seurat and scater R packages running in R version 4.1.2. After visual assessment of violin plots with quality metrics, thresholds for high-quality barcode retention were as follows: number of UMIs from 1000 to 30000, number of genes detected from 600, percent of mitochondrial reads up to 15%, percent of ribosomal genes up to 30%, percent of hemoglobin reads up to 0.1%, cell UMIs / Total > 0.2%, less than 50% of reads are from top 50 expressed gene. For rigorous doublet identification, 2 approaches were used: DoubletFinder version 2.0.4 and scDblFinder version 1.12.0 with an assumed doublet rate of 15%. Both tools should confirm that a cell is a singlet to be kept. Gene filtration included the removal of mitochondrial and hemoglobin genes, Dataset of right coronary artery plaque was composed of 5 individual runs and yielded 12538 after bad quality cells and doublets removal.","Sequence Alignment - FASTQ files for each sample were processed using 10X CellRanger software (v6.0.0), using Sus scrofa genome reference Ss11.1 (Ensembl gene build v109). Pseudogenes and small RNAs have been removed from the reference."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2000"],"pubmed_abstract":["The proliferation and phenotypic modulation of smooth muscle cells (SMCs) to alternative mesenchymal states is a key process by which atherosclerotic lesions grow. The underlying mechanisms can be studied in mouse and pig atherosclerosis, but it remains unclear to what extent the mesenchymal plaque cell types in these species recapitulate human disease. Here, we integrate published and new single-cell RNA sequencing data of plaque mesenchymal cells from human carotid and coronary arteries, pig aorta and coronary arteries, and mouse brachiocephalic arteries. By applying consensus across multiple integration and gene homology-matching strategies, we identify a conserved core continuum of mesenchymal plaque cells, ranging from SMCs to extracellular matrix-producing fibroblast-like cells, which is stable across species and vascular beds. Notably, several other populations differed between human and experimental lesions. Subpopulations of SMCs marked by DLX5 and RERGL expression were specific to human carotid and coronary plaques, respectively. Mesenchymal cell states with strong pro-angiogenic and inflammation-associated gene signatures were identified in pig, but not human, coronary plaque datasets, with the pro-angiogenic phenotype associated with early stages of necrotic core development. Pericytes were solely present in pig and human plaques, while chondrocyte-like cells were unique to mouse lesions. The presented interspecies maps of mesenchymal cell diversity, and their markers may inform translational research into the role of SMCs and their derived progeny in atherosclerosis."],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Sus scrofa"],"pubmed_title":["Mouse, pig, and human atherosclerotic lesions have common and distinct mesenchymal cell populations"],"pubmed_authors":["Jacob Fog Bentzon","Mouse, pig, and human atherosclerotic lesions have common and distinct mesenchymal cell populations Diana Sharysh, Paula Nogales Gomez-Imaz, Daniel Morales Cano, Anton Markov, Raul Izquierdo Serrano, Laura Carramolino Fitera, Julian Albarran-Juarez, Jacob Fog Bentzon","Paula Nogales","Diana Sharysh"],"additional_accession":[]},"is_claimable":false,"name":"Mouse, pig, and human atherosclerotic lesions have common and distinct mesenchymal cell populations","description":"The single-cell RNA-seq experiment aims to explore the cell-type composition of right coronary artery plaques to provide an overview of human-like atherosclerosis. The PCSK9 transgenic minipigs were subjected to 15 months of HFHC diet (HFHC group f, n=4; m, n=1). At the time of euthanasia, plaque parts without media were quickly processed and analyzed by scRNA-sequencing.","dates":{"release":"2025-08-30T00:00:00Z","modification":"2025-08-30T01:01:55.132Z","creation":"2025-08-08T14:04:22.032Z"},"accession":"E-MTAB-15464","cross_references":{"ENA":["ERP178564"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1101/2025.07.24.666663"]}}