Light-Seq transcriptome sequencing data. Mus musculus

We present a new approach, Light-Seq, for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding in fixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially-targeted, rapid photocrosslinking of DNA barcodes onto cDNAs in situ with a novel one-step DNA stitching reaction to create pooled, spatially-indexed sequencing libraries. This light-directed barcoding enables in situ selection of multiple cell populations in intact fixed tissue samples for full transcriptome sequencing based on location, morphology, or protein stains, without cellular dissociation. Applying Light-Seq to mouse retinal sections, we recovered thousands of differentially enriched transcripts from three adjacent cellular layers and discovered new biomarkers for a very rare neuronal subtype, dopaminergic amacrine cells, from only 4-8 individual cells per section. Light-Seq provides an accessible workflow to combine in situ imaging and protein staining with next-generation sequencing of the same cells, leaving the sample intact sample for further analysis post-sequencing.