biostudies-arrayexpressTallulah AndrewsMus musculusCellranger(v7.0.1), Seurat(v5.0.1)https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17061We assessed the sex-specific effects of elevated Lp(a) on the development and progression of atherosclerosis in a humanized mouse model. Wild-type and mice with a humanized LPA gene were subject to CRISPR-mediated Ldlr knock out and 24 weeks of high-fat, high-cholesterol diet to induce atherosclerosis. Diseased aortic cells were dissociated and pooled (2 animals per pool) then sorted for live-dead and subject to 3' single-cell RNAseq using 10X Chromium V3 chemistry. We identified significant changes in macrophage phenotype with an increase in contractility markers suggesting enhanced myeloid-myofibroblast transition in LPA+ mice.biostudies-arrayexpressSample Collection - Two aortas of a given sex and genotype were pooled, and surrounding adipose tissue manually removed. Remaining tissue was digested for 12 minutes at 37 degrees Celsius in digestion buffer containing collagenase I (Fisher Scientific, 450 U/mL), collagenase XI (Sigma, 125 U/mL), DNase I (Sigma, 60 U/mL), hyaluronidase (60 Sigma, U/mL), elastase (Sigma, 50 ng/mL) & actinomycin D (ThermoFisher, 5 µg/mL),  and the adventitial layer was gently removed from the aorta. The aorta was then minced into small pieces and placed into the digestion buffer again for at least 70 min at 37°C on a rotator. Cell suspensions were filtered through a 70-µm filter, washed, and resuspended in 5% FBS+PBS, followed by staining with SYTOXTM Blue (ThermoFisher) and then sorted to remove dead cells Nucleic Acid Extraction - 10,000 cells were loaded onto a 10X Chromium for scRNAseq using Next GEM Single-Cell 3’ Kit v3.1 at the London Regional Genomics Centre (London, Ontario). Libraries were sequenced to a depth of 400 million/reads per sample using the Illumina NovaSeq X – 10B flow cell at The Centre for Applied Genomics Next Generation Sequencing Facility (Toronto, Ontario).Sample Treatment - At 8-10 weeks of age mice were injected with AAV-CRISPR targeting mouse hepatic Ldlr and fed ad libitum high-fat, high cholesterol diet (42% calories from fat, 0.2% cholesterol) to induce atherosclerosis for 24 weeks.Library Construction - 10X Chromium for scRNAseq using Next GEM Single-Cell 3’ Kit v3.1Growth Protocol - Mice were housed a 23 deg Celsius with 12 hr light/dark cycle.Sequencing - Libraries were sequenced to a depth of 400 million/reads per sample using the Illumina NovaSeq X – 10B flow cell.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Fastq files were aligned and quantified using Cell Ranger (10X Genomics, v7.0.1), aligning to the mouse reference genome (mm10; release date: 2020) with (introns_and_exons) and without (exons_only) including introns.Data Transformation - Fastq files were aligned and quantified using Cell Ranger (10X Genomics, v7.0.1), aligning to the mouse reference genome (mm10; release date: 2020) with (introns_and_exons) and without (exons_only) including introns. UMI counts for introns_and_exons were manually QCed, normalized with sctransform, and clustered using Seurat(v5.0.1) and manually annotated using markers from existing literature.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNA10X Chromium Next GEM Single-Cell 3' Kit v3.1Illumina NovaSeq XAAV-CRISPRDigital Alliance of Canada10X Dual Index KitRNA-seq of coding RNA from single cellsMus musculusMarlys KoschinskyMichael BoffaTallulah AndrewsSunny PangJulia St. JohnfalseElevated Lipoprotein(a) levels dictate a unique plaque phenotype and transcriptomic signature in transgenic mice with advanced atherosclerosisWe assessed the sex-specific effects of elevated Lp(a) on the development and progression of atherosclerosis in a humanized mouse model. Wild-type and mice with a humanized LPA gene were subject to CRISPR-mediated Ldlr knock out and 24 weeks of high-fat, high-cholesterol diet to induce atherosclerosis. Diseased aortic cells were dissociated and pooled (2 animals per pool) then sorted for live-dead and subject to 3' single-cell RNAseq using 10X Chromium V3 chemistry. We identified significant changes in macrophage phenotype with an increase in contractility markers suggesting enhanced myeloid-myofibroblast transition in LPA+ mice.2026-09-17T00:00:00Z2026-09-25T13:36:47.758Z2026-05-20T15:12:54.778ZE-MTAB-17061ERP193644EFO_0002944EFO_0004170EFO_0003789EFO_0005684EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969