Project description:Using 23-months old mice of a inducible expression of human a-syn constructs based Parkinson mouse model, we produced a single nucleus RNA dataset by cutting 0mm Bregma to -5mm Bregma. The Chromium 3’ Single Cell Library Kit (10x Genomics) was used and Sequencing was performed on a NovaSeq 6000. Processed count matrices, metadata and objects with filtered, clustered, and annotated data can be found on Zenodo: 10.5281/zenodo.14988055
Project description:Using 6-months, 16-months, and 24-months old mice of a inducible expression of human a-syn constructs based Parkinson mouse model, we produced a single nucleus RNA dataset by cutting 0mm Bregma to -5mm Bregma. The Chromium 3’ Single Cell Library Kit (10x Genomics) was used and Sequencing was performed on a NovaSeq 6000.
Project description:These files represent single cell RNA-Seq data generated on a 10x Chromium genomics platform from three biological replicates from the embryonic day (E)18.5 developing mouse kidney and three biological replicates of iPSC-derived human kidney organoids differentiated according to our published protocol (Takasato et al., Nature Protocols 2016). When aggregated, the mouse data represents >6000 cells that passed our QC, containing most major cell types known to exist in the developing mouse kidney. The aggregated human organoid data contains of >7000 cells that passed our QC and contains populations representing endothelial cells, podocytes, stroma, nephron, and off-target populations with similarity to neurons.
Project description:In this study, we conducted a histopathological-based analysis of 10x Genomics Visium spatial transcriptomics data on a human kidney sample corresponding as closely as possible to the reality of the interpretation of a kidney biopsy in a healthcare or research context.
Project description:This study presents single-nucleus RNA sequencing data generated from postmortem human choroid plexus tissue. Isolated nuclei were profiled using the 10x Genomics Chromium platform to characterize gene expression across diverse cell populations of the choroid plexus. The resulting dataset provides a resource for investigating cell-type-specific transcriptional programs and cellular heterogeneity within the human choroid plexus in health and disease.
Project description:The craniopharyngioma tumor specimen was digested immediately after surgical resection, and a single-cell library was prepared using 10x Genomics. The obtained sequencing data were processed and analyzed using Cell Ranger.
Project description:The cell lines once in suspension were washed with PBS and pelleted by 5 minutes of centrifugation at 400g. The individual suspensions were filtered through a 35um mesh and their densities were adjusted to 106 cells/mL in PBS on ice. An equal volume of each suspension was pooled before being processed at the National Genomics Infrastructure (NGI, Scilifelab, Solna, Sweden). The cell processing consisted of proceeding with 10X Genomics V3.1 3’ dual index protocol according to manufacturer instruction (10X Genomics) and the libraries produced were sequenced on a NovaSeq XPlus (Illumina). The Fastq files were analyzed using zUMIs using a combined mouse and human genome which was built with STAR and consisted of the genomes GRCh38 and GRCm38 (mm10), with additional barcode capture (see yaml files in Code repository). The hashing barcodes were extracted using the tool UMIcountR29 and assigned to each cell. Based on the hashing barcodes and human and mouse gene usage per cell, cells were classified into the six conditions sequenced.