BaseScope ISH Assay 

The BaseScope ISH manual assay enables the visualization of a specific RNA locus at single cell sensitivity with spatial and morphological context. Used in applications such as the detection of exon junctions/splice variants, short/highly homologous RNA sequences (50-300 bases) and point mutations, the BaseScope assay can detect these in the single cell, in situ using a single Z pair, with down to a single (one) nucleotide difference. There are two types of BaseScope ISH assay, the BaseScope RED Assay and BaseScope Duplex Assay. 

BaseScope RED Assay

Detects short RNA targets, highly homologous sequences. RNA mutations, exon junctions, splice variants, circular RNA, and fusions.

Discern highly homologous MAGEA gene family within spatial morphological context.

Single ZZ probes specifically designed to recognize sequences within the variable region of the transcript. 

BaseScope Duplex Assay

Simultaneous visualization of two RNA targets while maintaining single cell resolution.

Identify gene edits, by duplexing RNA ISH cell marker probes and edit-specific probes (e.g. CRISPR/Cas9).

Visualize in vivo gene editing heterogeneity at the spatial transcriptome level.

Examples of BaseScope ISH Assay Applications

Splice variant detection of EGFRviii+ in glioblastoma with BaseScope V2 Assay

Exon Junctions / Splice Variants

Splice Variant Example: Detection of EGFRvIII+ in glioblastoma with the BaseScope v2 Assay

Gene Editing Example: Discern cell type-specific gene editing with the BaseScope Duplex Assay

Short Sequences

Gene Editing Example: Discern cell type-specific gene editing with the BaseScope Duplex Assay

Point Mutation Example: Detection of KRAS G12D in KRAS mutation cell line with the BaseScope v2 Assay

Point Mutations

Point Mutation Example: Detection of KRAS G12D in KRAS mutation cell line with the BaseScope v2 Assay