biostudies-arrayexpressMasahito YoshiharaMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14315To elucidate the mechanism of vascular repair, we performed single-cell analysis using the mouse vascular injury model (oxygen-induced retinopathy). In this model, mice were exposed to hyperoxic conditions at postnatal day 7 (P7) to induce ischemic retinopathy and the shedding of blood vessels. A return to normal oxygen conditions (normoxia) at P12 results in neovascularization that peaks at P17 and returns to normal by P30. CD31+/CD45neg vascular endothelial cells (ECs) were harvested at P12 (ischemic phase), P17 (retinopathy phase), and P25 (vascular repair phase) from retina only or retina plus optic nerve (6 samples) and analyzed together with corresponding control samples (total of 12 samples). Isolated tissues were digested, stained for CD31/CD45, and isolated by fluorescence-activated cell sorting (FACS). ECs were then loaded into the 10x Chromium Single Cell 3′ Kit (v3) to obtain approximately 5,000 cells per well.biostudies-arrayexpressLibrary Construction - ECs were then loaded into the 10X Chromium Single Cell 3′ Kit (v3) to obtain 5,000 cells per well, and library preparation was performed according to the manufacturer's protocol.Sequencing - The libraries were sequenced on an Illumina NovaSeq 6000 sequencer.Sample Collection - In the oxygen-induced retinopathy (OIR) model, wild-type C57BL/6J mice were exposed to 75% oxygen (hyperoxia) from P7 to P12 and returned to normal oxygen (normoxia) at P12. Retinal tissues and optic nerves were dissected from OIR and normoxic (control) mice at P12, P17, and P25. Tissues were digested with dispase I, type I collagenase, and type II collagenase. Cells were stained with anti-mouse CD31 and CD45 antibodies. Dead cells were stained with propidium iodide and excluded. CD31+CD45- vascular endothelial cells (ECs) were isolated by fluorescence-activated cell sorting (FACS).Nucleic Acid Extraction - ECs were then loaded into the 10X Chromium Single Cell 3′ Kit (v3) to obtain 5,000 cells per well, and library preparation was performed according to the manufacturer's protocol.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - The output count data were analyzed with the R package Seurat (v4.4.0) and normalized and scaled using the SCTransform function.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNA from single cellsMus musculusMasahito YoshiharaSusumu SakimotofalseSingle-cell RNA-seq of vascular endothelial cells in the mouse model of vascular injuryTo elucidate the mechanism of vascular repair, we performed single-cell analysis using the mouse vascular injury model (oxygen-induced retinopathy). In this model, mice were exposed to hyperoxic conditions at postnatal day 7 (P7) to induce ischemic retinopathy and the shedding of blood vessels. A return to normal oxygen conditions (normoxia) at P12 results in neovascularization that peaks at P17 and returns to normal by P30. CD31+/CD45neg vascular endothelial cells (ECs) were harvested at P12 (ischemic phase), P17 (retinopathy phase), and P25 (vascular repair phase) from retina only or retina plus optic nerve (6 samples) and analyzed together with corresponding control samples (total of 12 samples). Isolated tissues were digested, stained for CD31/CD45, and isolated by fluorescence-activated cell sorting (FACS). ECs were then loaded into the 10x Chromium Single Cell 3′ Kit (v3) to obtain approximately 5,000 cells per well.2025-11-21T00:00:00Z2025-11-21T06:12:47.12Z2024-07-30T09:33:18.634ZE-MTAB-14315ERP162823EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0003816EFO_0004184