De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution

We developed a spatially resolved RNA-seq protocol based on laser capture microdissection (LCM) and spatial barcoding strategy termed Spatial-seq. Here, we provide the demo transcriptomic data derived from mouse hypothalamus and isocortex regions for applications of our newly proposed spatial deconvolution algorithm termed Bulk2Space. We want to reveal the spatial heterogeneity and cellular diversity within the bulk brain region. We performed laser capture microdissection to isolate the hypothalamus and isocortex regions of mouse brain sections from the sagittal direction. The brain sections were first registered to the Allen Brain Atlas, and each main region was annotated. The annotated region outline was then imported into LCM. The hypothalamus and isocortex regions were cut by LCM and followed with RNA-seq to obtain the gene expression matrix.