Protocol for single-cell spatial transcriptomic profiling of cultured cells and engineered tissues without embedding or sectioning
The deposited data corresponds to the development of a protocol for spatial transcriptomic profiling of 2D engineered tissues and cell cultures that are not compatible with standard embedding and sectioning. By fixing and permeabilizing cells grown directly on a microscope glass slide, we demonstrate how Visium HD spatial gene expression kit can be used to investigate the function of these cells. Manuscript link: https://star-protocols.cell.com/protocols/4456 Github repository: https://github.com/HaylieHelms/vhd-scbioprint1 Overall design: A combination of primary human cells (mammary eptithelial cells, mammary myoepithelial cells, mammary fibroblasts, umbilical vein endothelial cells, and macrophages) and human cell lines (MDA-MB-231 and MCF10A) were patterned onto a collagen coated glass microscope slide using a single-cell bioprinter (Biopixlar, Fluicell). The cells were cultured in M87 media for 24 hours before being fixed with 4% PFA and permeabilized with 100% methanol. The Visium HD spatial transcriptomics protocol was then followed to generate the data deposited here.