Repository for: Single-cell spatial transcriptomic profiling of cultured cells and engineered tissues without embedding or sectioning
Description
Manuscript link: pending This repository contains, or provides links to, the code and associated data used to generate figures 3 and 4 of the manuscript. Due to limited storage space here, the experimental documentation, raw FASTQs, Space Ranger Inputs, and Space Ranger (v3.1.3) Outputs for the H&E dataset are available through Gene Expression Omnibus series accession number GSE296623 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE296623. The Loupe files, .csv annotation exports from Loupe, and code are provided here. Please note the cell type annotations are incomplete; PrintPattern "Random_TME_ALL" was annotated for the manuscript. Space Ranger was run again using an IF image, and the data is deposited here. *NOTE: The IF image is a live cell image (cells are transduced) taken right before fixation. The cells have migrated slightly between the image and when they were fixed (long scan/image acquisition time) so please proceed with extreme caution if using that version of the data since the image is slightly different than what was actually transferred to the capture area. This data was used only for illustrative purposes. I did not analyze any of the IF outs.