Project description:We developed an optimized, low-cost, split-pool barcoding-based multimodal profiling protocol based upon SHARE-seq (concurrent single-cell ATAC/RNA-seq). With SHARE-seq, we profiled human kidney samples from multiple different anatomical regions. Therefore, we develop a large-scale multimodal single-cell atlas for 3D anatomy of the human kidney.
Project description:Using Multiome and previously published sc/snRNA-seq data, we studied eight anatomical regions of the human heart including left and right ventricular free walls (LV and RV), left and right atria (LA and RA), left ventricular apex (AX), interventricular septum (SP), sino-atrial node (SAN) and atrioventricular node (AVN). For the first time, we profile the cells of the human cardiac conduction system, revealing their distinctive repertoire of ion channels, G-protein coupled receptors and cell-cell interactions. We map the identified cells to spatial transcriptomic data to discover cellular niches within the eight regions of the heart.
Project description:Using Multiome and previously published sc/snRNA-seq data, we studied eight anatomical regions of the human heart including left and right ventricular free walls (LV and RV), left and right atria (LA and RA), left ventricular apex (AX), interventricular septum (SP), sino-atrial node (SAN) and atrioventricular node (AVN). For the first time, we profile the cells of the human cardiac conduction system, revealing their distinctive repertoire of ion channels, G-protein coupled receptors and cell-cell interactions. We map the identified cells to spatial transcriptomic data to discover cellular niches within the eight regions of the heart.
Project description:Phylum Cnidaria is the oldest extant venomous group and is defined by the presence of nematocysts, specialised organelles responsible for venom production and delivery. While nematocysts and toxin peptides are distributed across the entire animal, nematocyst and venom profiles have been shown to differ across morphological structures in actiniarians. In this study, we explore the relationship between patterns of toxin expression and the ecological roles of discrete anatomical structures in Telmatactis stephensoni. Specifically, using a combination of proteomic and transcriptomic approaches, we examined whether there is a direct correlation between the functional similarity of regions and the similarity of their associated toxin expression profiles. We report that the regionalisation of toxin production is consistent with the partitioning of the ecological roles of venom across envenomating structures, and that three major functional regions are present in T. stephensoni— tentacles, epidermis and gastrodermis. Additionally, we find that structures which serve similar functions not only have comparable toxin profiles but also similar nematocyst types. There was no overlap in the toxins identified using proteomics and transcriptomics, however, the expression patterns of specific milked venom peptides were conserved across RNA-seq and mass spectrometry imaging datasets. Furthermore, based on our data, it appears that acontia of T. stephensoni may be transcriptionally inactive and only mature nematocyst are present in the distal portions of the threads. Overall, we find that the venom profile of different anatomical regions in sea anemones varies according to its ecological functions.
Project description:To study the effect of GLI3 knockout on early brain organoid development, we collected single-cell multiome data from 18 day old brain organoids