Fig. 1: Light-Seq overview.

Light-Seq enables selective barcoding of custom selected cells or tissue regions in situ for transcriptomic sequencing. Step (1): Target ROIs can be selected based on phenotypic factors including spatial location, morphology or protein biomarkers in automated or manual fashion after imaging. Custom selection allows large or small regions, and contiguous or disjointed cell groups to be flexibly labeled by photocrosslinking of DNA barcodes, which are then converted into sequenceable indices. For multiplexed targeting of different cell groups or regions, the process can be iterated using different barcode sets. Step (2): After light-directed labeling, barcoded cDNAs are released and prepared into pooled sequencing libraries which are read by standard NGS platforms. The obtained profiles can be analyzed to identify differentially expressed genes. Optionally, the same sample can be revisited after sequencing to perform follow-up assays, such as high-resolution imaging, morphology or protein labeling.