Light-Seq Cell Barcoding v3

• DOI: 10.17504/protocols.io.eq2ly77jplx9/v3
• Publication Date: 2022-12-19T22:26:03Z
• Authors: Jocelyn Y. Kishi; Ninning Liu; Emma R. West; Kuanwei Sheng; Jack J. Jordanides; Matthew Serrata; Constance L. Cepko; Sinem K. Saka; Peng Yin
• Keywords: DNA Barcoding; Illumina dye sequencing

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