| Popis: |
Spatial transcriptomics enables the study of localization-indexed gene expression activity in tissues, providing the transcriptional landscape that in turn indicates the potential regulatory networks of gene expression.In situsequencing (ISS) is a targeted spatial transcriptomic technique, which is based on padlock probe and rolling circle amplification combined with next-generation sequencing chemistry, for highly multiplexedin situgene expression profiling. Here, we present improvedin situsequencing (IISS) that exploits a new probing and barcoding approach, combined with advanced image analysis pipeline for high-resolution targeted spatial gene expression profiling. We developed an improved combinatorial probe anchor ligation chemistry using a 2-base encoding strategy for barcode interrogation. The new encoding strategy resulted in higher signal intensity as well as improved specificity forin situsequencing, while maintaining a streamlined analysis pipeline for targeted spatial transcriptomics. We showed that IISS can be applied to both fresh frozen tissue and formalin-fixed paraffin embedded tissue sections for single cell level spatial gene expression analysis, based on which the developmental trajectory and cell-cell communication networks can also be constructed. In conclusion, our method is a versatile molecular tool for targeted spatial transcriptomic analysis. |
