Protocol for using MULTILAYER to reveal molecular tissue substructures from digitized spatial transcriptomes

Highlights

• MULTILAYER reveals spatial transcriptomes (ST) into biologically relevant substructures

• MULTILAYER provides a user-friendly environment for ST processing

• MULTILAYER has been used on a variety of data, including high-resolution ST

• A “Visium data convertor” and a “high-resolution data compressor” are also available

Summary

Spatially resolved transcriptomics (SrT) allow researchers to explore organ/tissue architecture from the angle of the gene programs involved in their molecular complexity. Here, we describe the use of MULTILAYER to reveal molecular tissue substructures from the analysis of localized transcriptomes (defined as gexels). MULTILAYER can process low- and high-resolution SrT data but also perform comparative analyses within multiple SrT readouts.

For complete details on the use and execution of this protocol, please refer to Moehlin et al., 2021.