A method for spatially resolved tissue transcriptomics applied to the mouse and lizard P. vitticeps brains
We have developed an imaging-free framework to localize nucleic acids within a tissue by combining  a compressed sensing tissue-sampling strategy based on multi-angle-sectioning and an associated image reconstruction algorithm.  Initially, the tissue is cut into consecutive thin slices. Subsequently these are further sliced along an orthogonal plane at predefined orientations resulting in tissue strips that are subject to RNA sequencing. We implemented this framework to transform a single-cell RNA sequencing protocol into an imaging-free spatial transcriptomics technique. The method was validated by profiling the transcriptome of the Murine brain, and used to spatially profile the brain transcriptome of the Australian Central bearded dragon, Pogona vitticeps. Overall design: One Mus musculus and one Pogona vitticeps brain in thin coronal sections, cut into stripes at several alternating angles Please note that the 'GSE152989_new_suppl_files.tar.gz' contains the expression data formatted in ".cef" format. The "cef" is a tab delimited file format described at: https://github.com/linnarsson-lab/ceftools