{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["zeng linjun"],"organism":["Sus scrofa"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15847"],"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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Left atrial appendage (LAA) tissues were collected from Bama miniature pigs (Sus scrofa) following a survival period of over ten months post-magnetofluid occlusion. Tissues were dissected into two regions: the contact zone (tissue in direct contact with the implanted magnetogel) and the non-contact zone (adjacent tissue not in direct contact). All procedures were approved by the Institutional Animal Care and Use Committee.","Sequencing - The constructed single-cell RNA-seq libraries were sequenced on an Illumina platform using a paired-end read configuration. The sequencing strategy ensured that Read 1 contained the cell barcode and UMI sequence, while Read 2 contained the cDNA insert.","Nucleic Acid Extraction - Single-cell suspensions were prepared from harvested LAA tissues through meticulous mincing and enzymatic dissociation using a defined cocktail of collagenase and DNase. The cell suspension was filtered through a cell strainer to remove debris. Cell viability and concentration were assessed using standard Trypan Blue staining and counting methods. The resulting single-cell suspension was used directly for single-cell library construction without intermediate RNA extraction.","Library Construction - Single-cell RNA sequencing libraries were constructed using the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kit according to the manufacturer's instructions. Single-cell suspensions were combined with Master Mix and loaded onto a Chromium Chip to generate gel beads-in-emulsion (GEMs). Following GEM cleanup and cDNA amplification, the libraries were constructed through enzymatic fragmentation, end-repair, A-tailing, adapter ligation, and sample index PCR. Final libraries were quantified and quality-controlled to confirm the expected library size distribution."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Single-cell RNA-seq data were processed using SCTransform normalization with regularized negative binomial regression. Quality control included filtering cells with 200-6,500 genes and <10% mitochondrial content. Doublets were removed using scDblFinder. Batch effects between ContactZone and NonContactZone samples were corrected using reciprocal PCA (RPCA) integration. Data were scaled, 30 principal components were selected, and clustering was performed at resolution 0.3. Cell types were annotated based on canonical marker genes."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Sterile surgical instrument set (scalpels, tissue forceps, dissection scissors), animal operating table, biological safety cabinet","10x Genomics Chromium Controller, PCR thermocycler, Agilent 2100 Bioanalyzer with High Sensitivity DNA chip (for quality control)","Illumina NovaSeq 6000","Water bath (for enzymatic dissociation), cell strainer (70-μm), benchtop centrifuge, automated cell counter/hemocytometer, biological safety cabinet"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Sus scrofa"],"pubmed_authors":["zeng linjun"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell RNA sequencing analysis of left atrial appendage tissue following magnetogel-based occlusion in a porcine model","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.","dates":{"release":"2025-12-07T00:00:00Z","modification":"2026-05-27T15:36:25.732Z","creation":"2025-10-24T13:13:29.569Z"},"accession":"E-MTAB-15847","cross_references":{"ENA":["ERP182886"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}