Spatial multi-omics at subcellular resolution via high-throughput in situ pairwise sequencing
Our research group has successfully developed an efficient high-throughput dual-end in situ sequencing-based spatial omics technology. We have established both an in situ spatial omics platform and a targeted spatial omics platform. This method employs padlock probes designed to directly target specific molecular sequences, followed by RNA-dependent DNA ligation to form circularized probes, and then signal amplification through rolling circle amplification (RCA). Additionally, we have upgraded the traditional single-barcode encoding system to a dual-barcode combinatorial encoding system, thereby significantly increasing the detection throughput per round. As a result, this technology can decode 10 targets in a single sequencing round and 10^N genes over N rounds. Compared to existing in situ sequencing methods (which typically detect 4N genes), our approach greatly improves both efficiency and throughput while reducing signal loss. Preliminary results have demonstrated that using our dual-end in situ sequencing technology, MIP-Seq, we have already achieved in situ detection of 100 genes in hypothalamic tissue with only two sequencing rounds.