biostudies-arrayexpressRebecca EmbalabalaMus musculusCellRangerhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16239This study investigates Alzheimer's Disease-related transcriptomic changes in brain endothelial cells of 5XFAD mice on the C57BL/6J background using single-cell RNA sequencing. Brains from male hemizygous 5XFAD (n=3) and wild-type control mice (n=3) aged 12 months were used. Brain tissue (excluding olfactory bulbs and cerebellum) was dissociated into a single cell suspension, and Fluorescence Activated Cell Sorting (FACS) was used to isolate CD31+, CD45- cells. Cells were encapsulated and sequenced using the 10x Genomics platform. Libraries were sequenced on an Illumina NovaSeq XP, targeting ~50,000 reads per cell. In our analysis, raw data were aligned to the mouse (GRCm39)-2024-A reference genome. FASTQs are named: 13389-RE-1 (Wild-type 1), 13389-RE-2 (Wild-type 2), 13389-RE-3 (Wild-type 3), 13389-RE-4 (5XFAD 1), 13389-RE-5 (5XFAD 2), 13389-RE-6 (5XFAD 3).biostudies-arrayexpressNucleic Acid Extraction - Following Fluorescence Activated Cell Sorting (FACS), total RNA was extracted from the isolated CD31+, CD45- brain endothelial cells. Nucleic acid isolation was performed according to the manufacturer's protocol.Sample Collection - Brains from male hemizygous 5XFAD (n=3) and wild-type control mice (n=3) aged 12 months were used. Brain tissue (excluding olfactory bulbs and cerebellum) was dissociated into a single cell suspension, and Fluorescence Activated Cell Sorting (FACS) was used to isolate CD31+, CD45- cellsLibrary Construction - Single-cell gene expression libraries were generated using the 10x Genomics Chromium Next GEM Single Cell 5'Gene Expression, v2 Chemistry kit. Libraries were prepared according to the manufacturer's protocol, and raw data were later processed using Cell Ranger against the GRCm39-2024-A referenceSequencing - Nucleic acid sequencing was performed on an Illumina NovaSeq X Plus (NovaSeq XP) system. The run followed the manufacturer's recommended parameters for the 10x Genomics 5',v2 chemistry. The minimum sequencing depth target was ~50,000 paired-end reads per cell.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw sequencing data (FASTQ files) were processed using 10x Genomics Cell Ranger pipeline. Reads were aligned to the mouse reference genome GRCm39-2024-A.MetabolomicsUnknownTranscriptomicsGenomicsProteomics5-Laser BD FACSAria IIIIllumina NovaSeq XNone10X Genomics ChromiumRNA-seq of coding RNA from single cellsMus musculusEthan LippmannRebecca EmbalabalafalseSingle-Cell RNA Sequencing of Brain Endothelial Cells in 12-Month-Old Male 5XFAD and Wild-Type MiceThis study investigates Alzheimer's Disease-related transcriptomic changes in brain endothelial cells of 5XFAD mice on the C57BL/6J background using single-cell RNA sequencing. Brains from male hemizygous 5XFAD (n=3) and wild-type control mice (n=3) aged 12 months were used. Brain tissue (excluding olfactory bulbs and cerebellum) was dissociated into a single cell suspension, and Fluorescence Activated Cell Sorting (FACS) was used to isolate CD31+, CD45- cells. Cells were encapsulated and sequenced using the 10x Genomics platform. Libraries were sequenced on an Illumina NovaSeq XP, targeting ~50,000 reads per cell. In our analysis, raw data were aligned to the mouse (GRCm39)-2024-A reference genome. FASTQs are named: 13389-RE-1 (Wild-type 1), 13389-RE-2 (Wild-type 2), 13389-RE-3 (Wild-type 3), 13389-RE-4 (5XFAD 1), 13389-RE-5 (5XFAD 2), 13389-RE-6 (5XFAD 3).2025-12-31T00:00:00Z2026-05-27T15:34:23.596Z2025-11-21T13:42:29.31ZE-MTAB-16239ERP185478EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0003816EFO_0004184