BaseScope™ assay can discern between short variable sequences of the different CDR3 regions. The single ZZ probes are specifically designed to recognise sequences within the variable region of the CDR3 transcript.

BaseScope™ assay can discern between short variable sequences of the different CDR3 regions. The single ZZ probes are specifically designed to recognise sequences within the variable region of the CDR3 transcript.

Representative images of CDR3 with the BaseScope™ Assay. Jurkat-specific CDR3α probe only recognize the TCR in Jurkat T cells and do not recognize the TCR in CCRF T cells.

Representative images of CDR3 with the BaseScope™ Assay. Jurkat-specific CDR3α probe only recognize the TCR in Jurkat T cells and do not recognize the TCR in CCRF T cells.

Representative images of CDR3 with the BaseScope™ Assay. Jurkat-specific CDR3β probe only recognize the TCR in Jurkat T cells and do not recognize the TCR in CCRF T cells.

Representative images of CDR3 with the BaseScope™ Assay. Jurkat-specific CDR3β probe only recognize the TCR in Jurkat T cells and do not recognize the TCR in CCRF T cells.

The BaseScope™ Reagent Kit v2-RED, is based on ACD’s patented signal amplification and background suppression technology. The assay uses a novel and proprietary method of in situ hybridization (ISH) to visualize single RNA molecules per cell in a multitude of sample types mounted on slides. The BaseScope™ Assay is used for the detection of short RNA targets (50-300 bases), highly homologous sequences, RNA mutations, and exon junctions for the detection of splice variants, circular RNA, and gene fusion. The BaseScope™ Assays do not require an RNase-free environment that is used for traditional RNA ISH. 

Applications of the BaseScope™ RED Assay

Exon Junctions/ Splice VariantsShort/Homologous Target SequencesPoint Mutations*
Exon junctions/splice variantsShort targets/highly homologous gene sequences (50-300nt)Point mutation
Circular RNA (cirRNA)T cell receptors (TCRs) and CDR sequences in T-cell clonesShort InDel
Gene fusionpre-miRNAHomologues
Gene knockout (KO)Gene editing/CRISPR* ACD Validated Point Mutations Only

 

One major application for the BaseScope™ RED Assay is to identify highly homologous short target sequences. The BaseScope™ RED Assay can discern highly homologous MAGEA gene family in intact tissue with morphological context.

 

BaseScope™ Probes for MAGEA Gene Family Detection

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The BaseScope™ Reagent Kit v2-RED with Fast Red dye offers high contrast and easy dot visualization. 
The BaseScope™ Assay Workflow Requires:

BaseScope™ Target Probes (Catalog or Made-to-Order C1 Probes)
BaseScope® Control Probes (Select positive control probes and negative control probes)
Control Slides (optional)
BaseScope™ Reagent Kit v2-Red (Universal Pretreatment Kit, Detection kit, and Wash Buffer included)
Brightfield microscope or multispectral fluorescent imaging system
HybEZ™ I or II Hybridization System

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