biostudies-arrayexpressLiu FangyanRattus norvegicushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15343To map the cell type-specific transcriptome landscape of the inflammatory microenvironment induced by systemic injection of lipopolysaccharide (LPS), we analyzed the hippocampus of aged rats on day 3 following a single injection to identify key molecules within specific cell subsets by single-cell RNA sequencing (scRNA-seq).biostudies-arrayexpressLibrary Construction - Single-cell RNA libraries were prepared using the 10x Genomics Chromium Single Cell 3’ v3 kit, following the manufacturer’s protocol. Briefly, single cells were partitioned into gel beads in emulsion (GEMs), reverse transcription and cDNA amplification were performed, followed by library construction.Sequencing - Libraries were sequenced on the Illumina NovaSeq 6000 platform using paired-end (PE) 150 bp reads. Base calling and quality control were performed using Illumina software.Nucleic Acid Extraction - Single-cell suspensions were prepared from dissected hippocampal tissues, followed by RNA extraction using the [StepOnePlus Real-Time PCR System] according to the manufacturer’s instructions. RNA quality was assessed by Bioanalyzer (Agilent).Sample Collection - Pair of hippocampi from LPS and NC group rats(n = 3 per group) were harvested on day 3 after LPS injection and pooled by group for scRNA-seq. Briefly, rats were anesthetized and perfused through the heart with ice-cold PBS. The hippocampus was immediately isolated and enzymatically dissociated using the Adult Brain Dissociation Kit according to the manufacturer’s instructions (Miltenyi Biotec, 130-107-677). After removal of debris and red blood cells, the suspended single cells were collected in Dulbecco’s phosphate buffered saline (DPBS) supplemented with 0.04% bovine serum albumin. Cells were stained with trypan blue and the proportion of viable cells (unstained) was determined using a Luna-FL™ automated cell counter (Logos Biosystems, Anyang, Kyonggi-do, South Korea). Samples with viable cell counts above 85% were loaded onto a 10x Genomics Chromium chip according to the manufacturer's instructions.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - cRNA-seqdata were further analyzed using 10x Cell Ranger (version2.2.0,https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cellranger), processed with unique molecular identifiers (UMI) tools, and aligned to the rat reference genome using STAR (Spliced Transcripts Alignment to a Reference). Data normalization, detailed analysis, and visualization were performed using the Seurat package. For initial quality control of the extracted gene-cell matrices, we filtered cells using Seurat parameters as below: i) nFeature_RNA >200 & nFeature_RNA <8,000 for number of genes per cell; ii)percentage of mitochondrial genes less than 20%; iii) minimum expressing cells = 3. Results were then normalized to total expression and log-transformed. Principal component analysis was conducted using the Seurat R Package to identify the first 20 principal components in the feature-barcode matrices for dimensionality reduction. Next, t-distributed stochastic neighbor embedding (t-SNE) and the Uniform Manifold Approximation and Projection (UMAP) algorithm were used for visualization of the reduced data in two-dimensional space and expression similarity analysis, respectively.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNA from single cellsRattus norvegicusLiu FangyanfalseSingle-Cell Profiling of the Inflammatory Microenvironment in the Aged Rats Hippocampus and the Contributions of Cerebrovascular Endothelial CellsTo map the cell type-specific transcriptome landscape of the inflammatory microenvironment induced by systemic injection of lipopolysaccharide (LPS), we analyzed the hippocampus of aged rats on day 3 following a single injection to identify key molecules within specific cell subsets by single-cell RNA sequencing (scRNA-seq).2026-03-28T00:00:00Z2026-03-28T02:03:54.814Z2025-07-09T14:58:31.097ZE-MTAB-15343ERP175148EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0003816EFO_0004184