Dysregulation of MMP2-dependent TGF-ß2 activation impairs fibrous cap formation in type 2 diabetes associated atherosclerosis
type: Dataset
distribution: Landing page for the dataset
description: Cohort description: Human carotid plaques used in this study were obtained from the Carotid Plaque Imaging Project biobank (Malmö, Sweden; ClinicalTrials.gov ID NCT05821894). These plaques were collected from patients undergoing carotid endarterectomy (CEA) at Skåne University Hospital's Vascular department in Malmö, Sweden. The indications for surgery were: plaques associated with ipsilateral symptoms (transitory ischemic attack, stroke, or amaurosis fugax) and a degree of stenosis greater than 70% (measured by duplex ultrasound), or plaques from asymptomatic patients, with a degree of stenosis greater than 80%. The study has received ethical approval, and all patients provided oral and written informed consent. All work involving human subjects adheres to the principles of the 1975 Declaration of Helsinki. Dataset description: - Bulk RNA sequencing was performed on carotid plaques from patients with type 2 diabetes (T2D). Total RNA was extracted with the Trizol method, and libraries were prepared using the ScriptSeq™ v2 Kit. Sequencing was performed on Illumina HiSeq2000 and NextSeq platforms. Reads were aligned to the GRCh38 genome with STAR and quantified using Salmon with GENCODE V27 annotations. Counts were normalized with edgeR and expressed as log2-transformed counts per million (CPM) after batch corrected for sequencing platforms. - Single-cell transcriptomes were generated from human atherosclerotic plaque cells. Live cells were stained for CD45 and FACS sorted into 384-well plates, separating CD45+ and CD45- populations. RNA libraries were prepared and sequenced using the SmartSeq2 protocol at the SciLife Eukaryotic Genomics Facility. Cells with fewer than 10,000 raw reads, fewer than 500 detected genes, or more than 15% ERCC RNA Spike-In were excluded. Counts were log-normalized, scaled, and the top 2000 highly variable genes were used for dimensional reduction. - Spatial transcriptomics was performed on 10µm carotid plaque sections using the Visium Spat…
modified: 2024-06-24T00:00:00Z
issued: 2024-06-24T00:00:00Z
publisher: Lund University
theme: HEAL
access rights: NON PUBLIC
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  agent: Pratibha Singh
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    account: https://orcid.org/0000-0001-6814-1297
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  agent: Marju Orho-Melander
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  agent: Jan Nilsson
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  had role: principalInvestigator
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  agent: Andreas Edsfeldt
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keyword: Cardiology (incl. cardiovascular diseases)

Landing page for the dataset
type: Distribution
title: Landningssida för datasetet @sv
access URL: Dysregulation of MMP2-dependent TGF-ß2 activation impairs fibrous cap formation in type 2 diabetes associated atherosclerosis
availability: stable

Lund University
type: Agent
name: Lunds universitet @sv
type: Academia-ScientificOrganisation
source: 012a77v79