Single-cell and spatial mapping Identify cell types and signaling Networks in the human ureter

Protocols for single-cell RNA-seq and spatial gene expression integration and interactive visualization

“… Calculate highly variable genes. Filter the main count matrix for genes that are all 2 highly variable, 3 expressed in more than 3% of cells, and 1 have a mean expression > 0.4 in cells expressing the gene in question. PCA is then invoked on those genes.…”

“…Additionally, we have provided test data to perform this protocol from Fink et al. 1 As long as the appropriate files are prepared, this protocol should work with any pair of matching scRNA-seq and Visium dataset.…”

“…Both the scRNA-seq and Visium expression data have been processed according to Fink et al. 1 The data is provided in two ways – one through a release on GitHub and another via GEO submission.…”

Processing and cryopreservation of human ureter tissues for single-cell and spatial transcriptomics assays

“…This single-cell dissociation protocol has been optimized to obtain cells from different cellular compartments within the adult human ureter; including the basic cell types of the stroma, epithelial, and immune compartments. 1 From a 1 cm length of human ureter, the expected cell yield is typically ∼250,000 cells with a viability of > 90%, which is sustainable after cryopreserving and thawing. Furthermore, the basic cell types of the stroma, epithelial, and immune compartments are nearly identical before and after cryopreservation.…”

Organoid-based single-cell spatiotemporal gene expression landscape of human embryonic development and hematopoiesis

“…Pairing these datasets with the stem-cell-derived embryos deciphers cell-cell interactions in development. The recent emergence of spatial transcriptomics technology has generated various tissue atlas across various species (Asp et al, 2019; Chen et al, 2021; Fawkner-Corbett et al, 2021; Fink et al, 2022; Mantri et al, 2021; Maynard et al, 2021; Moses and Pachter, 2022; Tower et al, 2022; Zhao et al, 2022). Spatial transcriptomics can faithfully restore the original spatial location, allowing us to unravel the functional niche and explore the cellular signaling interactions.…”