What is seqFISH?

seqFISH (sequential Fluorescence In Situ Hybridization) is a technology that enables the identification of thousands of molecules like RNA, DNA, and proteins directly in single cells with their spatial context preserved. 

seqFISH applications result in a super-resolved image of genomic-level processes at work with high efficiency and accuracy. Image-mapping tissues with seqFISH identifies relationships between chromosome structures, chromatin states, gene expression, external and internal chemical signaling, and cell structure.

How seqFISH Works

To achieve ultra-resolution imaging of cell activity, we target thousands of single molecules with fluorescent probes. These probes are designed to find and hybridize with complementary DNA or RNA sequences in the tissue sample. This method can be applied to mRNA, DNA, or proteins.

By applying sequential rounds of fluorescent hybridization and imaging, we can readout thousands of individual locations as a temporal barcode. We then decode these barcodes to map the cell’s activity. These barcodes are represented as different colored dots (termed pseudocolors) in the final image.

Why seqFISH is Changing Genomics

To understand the ecology and micro-environment of tissues, we have to map the spatial organization of cell types and their interactions at the single cell level. seqFISH can multiplex over 10,000 molecules and integrate multiple modalities, such as imaging the transcriptome and proteins.

Single molecule imaging ensures absolute quantitation – each appears as a single dot in cells and abundance is quantified by counting the number of observed dots. There is no reverse transcription or PCR amplification required, which can bias quantification in traditional RT-PCR and RNA sequencing. In addition, seqFISH can accurately detect low copy number genes, such as transcription factors and master regulators, that cannot be detected with single cell RNAseq or immunostaining.

seqFISH can be applied to virtually any tissue type without preselecting genes, enabling unbiased discovery of genes that are relevant to biological phenomena. seqFISH can be combined with other technologies, like that of MEMOIR – a genetic application that encodes information into living systems, recording gene-expression states over time.