Project description:This project used snRNA-seq and Molecular Cartography (single cell spatial transcriptomics) to investigate the relation between morphology and molecular identity in human brain organoids.
Project description:Single cell ATAC-seq of PBMC - resting and stimulated. Used for comparison to asses the capabilies of the five-prime sequencing method in the detection of cis-regulatory elements using SCAFE (see publication).
Project description:We performed an inter-species comparison of murine spermatogenesis using the inbred strains C57B6J, CAST/EiJ and CAROLI/EiJ to investigate the cell type-specific evolution of gene expression levels among closely related species. We also used F1 crosses of C57B6J and CAST/EiJ to investigate context-specific regulatory effects on gene expression in cis and trans by measuring allele-specific expression (Goncalves et al. 2012; Wittkopp et al. 2021). To this end, single-cell RNA-Sequencing data was generated from dissociated testicular tissue in each mouse strain using the 10x Genomics scRNA-Seq platform.
Project description:These datasets are test datasets of sample-multiplexed scRNA-seq, consisting of cDNA (transcriptome) and sample barcode read files: Three-sample multiplexing experiment (JS009) is a MULTI-seq dataset containing mesenchyme embryonic hind limb bud cells, embryonic stem (ES) cells, and NIH3T3 cells. Each cell sample was labelled with a distinct MULTI-seq barcode. The barcode sequences were, CATAGAGC, TCCTCGAA, and GTGTACCT for the limb bud mesenchyme cells, the ES cells, and the NIH3T3 cells, respectively. Two-sample multiplexing experiment (JS010) is a CellPlex detaset, containing ES cells and NIH3T3 cells. Each cell sample was labelled with the 3'CellPlex Kit (10X Genomics). NIH3T3 cells and ES cells were labelled with CMO301 and CMO302, respectively.
Project description:Single cell five-prime end sequencing of PBMC - resting and stimulated. Used to asses the five-prime sequencing method in the detection of cis-regulatory elements using SCAFE (see publication)
Project description:The goal of the experiment is to determine whether it is feasible to use the 10x Genomics Gene Expression Flex solution in samples containing a mixture of human and mouse cells. First we tested how the presence of mouse cells impacted the data recovered by the use of the human whole trasnscriptome amplification (WTA) probe sets. Then we profiled a mixed species sample by using human and mouse probe sets in the same reaction. Finally, for samples with lower amounts of human cells we tried to correct the amount of cells recovered by the human and mouse probe sets by adjusting the amount of cells loaded from the respective hybridizations.
Project description:Induced pluripotent stem cells (iPSC) derived from fibroblasts of two healthy individuals were differentiated into NPC. Cells were profiled by scRNA-seq.
Project description:We characterised the transcriptomic profiles of 146,133 individual cells (post-QC) from whole rabbit embryos spanning gestational days 7, 8 and 9. These experiments were performed to elucidate the molecular programmes underlying gastrulation and early organogenesis in a non-rodent mammal. Combined with existing datasets of early mouse development, our rabbit developmental atlas facilitates a broad cross-species approach to deciphering early human development. Cell libraries were prepared using the 10X Genomics Chromium platform.