In situ sequencing for RNA analysis in preserved tissue and cells

A method based on in situ sequencing by ligation enables direct reading of short segments of RNA or sequence tags in preserved tissue sections and cells. Tissue gene expression profiling is performed on homogenates or on populations of isolated single cells to resolve molecular states of different cell types. In both approaches, histological context is lost. We have developed an in situ sequencing method for parallel targeted analysis of short RNA fragments in morphologically preserved cells and tissue. We demonstrate in situ sequencing of point mutations and multiplexed gene expression profiling in human breast cancer tissue sections.