Introducing BaseScope Assays
Detect exon junctions and short target sequences like never before — with morphological context.

BaseScope Assay

The BaseScope Assay is a new product from ACD, based on the same platform of proven and established RNAscope® technology, cited in over 500 publications in just 5 years. This new powerful assay provides new data dimensions and unique insight into biological mechanisms. The BaseScope Assay enables applications such as the detection of exon junctions in FFPE tissue with morphological context and the ability to visualize gene expression for short RNA target sequences (as short as 50bp)

With ACD's continued commitment to provide researchers advanced capabilities of performing RNA ISH, the development of the BaseScope product provides a key benefit to detect biological events in situ using a single ZZ pair (i.e. RNA sequence spanning 50bp). The BaseScope assay is developed with advances in probe design leveraging core concepts of the ZZ patented technology and applies a novel amplification system that generates increased signal with simultaneous background noise suppression.

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These technological advantages enable:
  • Detection of a specific RNA locus at single molecule detection sensitivity
  • Sensitive and specific detection of any exon junction
  • Detection of difficult targets like degraded RNA, transiently expressed RNA, and RNA in bone samples
  • Analysis of broad sample types, including FFPE tissues (including TMAs) and fresh frozen tissues




Exon junction detection

Technology overview:
Detection of exon junctions in single cells within the tissue environment is possible by using only one ZZ probe uniquely designed on the specific exon junction of interest. For an example of the detection of a sequence with specific exon skipping, METΔ14 (Frampton GM et al, Cancer Discovery, 2015; Awad MM et al, J Clin Oncol, 2016) where 3 probes are designed (image 1): one control probe designed for an exon junction present in all MET transcripts (exon junction 12/13), one probe designed for the exon junction with exon 14 (exon junction 14/15), and one probe designed for the exon junction with exon 14 skipping (exon junction 13/15). Figure 2 shows an example of the BaseScope assay used for the detection of METΔ14 in cell lines.

Application:
This strategy can be used for splice variant detection as well as other applications such as the confirmation of sequence after specific knock-out (KO) or detection of circular RNA at single cell level with morphological context (figure 3).

What to order:
Exon junction detection using the BaseScope assay is available through ACD's Pharma Assay Services. The following products can also be ordered to perform the analysis in your own lab:
BaseScope product for exon junction
BaseScope Reagent Kit-RED (includes pretreatment reagents for FFPE and Fresh Frozen Tissues)
Example of a few BaseScope Catalog Probes in this category:
322900
BaseScope Catalog Probes are available for:
• AR
• ERBB2
• IFNG
• IL4, IL6, IL10
• TNF
 
BaseScope Custom Probes 700001
BaseScope Set up Fee for Custom Probes 322972
VectaMount Mounting Medium 321584
BaseScope Control Probe Pack
(include 4 probes: PPIB probes 3zz, PPIB 1zz, DapB 3zz , DapB 1zz)
322975 (Human)
322976 (Mouse)

Contact your account manager to arrange a Pharma Assay services project or to order the product

Contact

 

 

 


FIGURE 1: Probe design for the detection of METΔ14 using the BaseScope assay. One ZZ probe (blue), designed to detect the junction between exons 12 and 13, is considered common and will detect both wild-type MET and METΔ14 mRNA. A second ZZ probe (orange) is designed to detect the junction between exons 14 and 15 and will detect only MET mRNA containing exon 14 (wild-type MET). A third ZZ probe is designed to detect the junction between exons 13 and 15 and will detect only MET exon 14 skipped mRNA (METΔ14). The 3 probes are tested in parallel (see next image).

FIGURE 2: Detection of METΔ14 using the BaseScope Assay. The cell lines H596 (METΔ14) and A549 (MET WT for exon 14) were used to examine METΔ14 status. The probe for exon junctions 12/13 showed expression of exons 12 and 13, which are present in both wild-type MET and METΔ14 cell lines. The probe for exon junction 13/15 detected expression of METΔ14 only in the H596 cell line. The probe for exon junction 14/15 detected expression of wild-type MET in the A549 cell line only. The negative control assay dapB was negative in both cell lines.

FIGURE 3: Detection of circular RNA using the BaseScope Assay. A single ZZ probe assay is designed at the specific junctions of the exons present within the circular RNA.

 


Short target sequences

Technology overview:
Single cell detection of short target sequences (50 to 300 bases) in the tissue environment is possible by using 1 to 6 ZZ probes per target of interest (figure 1).

Application:
The BaseScope assay can be used for the detection of short target sequences (figure 1) with morphological context, such as the CDR sequence for T cell receptor (TCR) clones (figure 2), snoRNA, pre-miRNA, or gene therapy. It can also be used to analyze highly homologous gene sequences, partially degraded RNAs (i.e., RNA extracted after decalcification from bone samples), or transiently expressed RNAs.

What to order:
Detection of short target sequences using the BaseScope assay is available through ACD's Pharma Assay Services. The following products can also be ordered to perform the analysis in your own lab:
BaseScope product for short target
BaseScope Reagent Kit-RED (includes pretreatment reagents for FFPE and Fresh Frozen Tissues)
Example of a few BaseScope™ Catalog Probes in this category:
322900
BaseScope Catalog Probes are available for:
• MAGEA
• APOBEC3
• XPB1
• LILRB2
• PRAM
 
BaseScope Custom Probes 700001
BaseScope Set up Fee for Custom Probes 322972
VectaMount Mounting Medium 321584
BaseScope Control Probe Pack
(include 4 probes: PPIB probes 3zz, PPIB 1zz, DapB 3zz , DapB 1zz)
322975 (Human)
322976 (Mouse)

Contact your account manager to arrange a Pharma Assay services project or to order the product

Contact

 

 

 


FIGURE 1

FIGURE 2: Detection of CDR3 α and β in the Jurkat T-cell line. Four BaseScope assays were designed to detect both the sense and anti-sense sequences of CDR3 α and β present in Jurkat cell lines. The Jurkat-CDR3α and β anti-sense probes detected expression in the Jurkat T-cell line, whereas the sense probes detected little to no signal.

 


RNAscope® Assay and BaseScope Assay comparison

RNAscope® Assay BaseScope Assay
Number of ZZ Pair per target
Standard probe design is 20 ZZ probes (minimum of 6 ZZ probes)

1 to 6 ZZ probes based on the application
Target mRNA >300 bases
lncRNA > 300 bases
RNA 50 to 300 bases
Exon junction
Application lcnRNA and mRNA >300 bases Short RNA, splice variants, circular RNA, CAR-T cell validation and detection, highly homologous sequences, CDR sequence for T cell clone (TCR), snoRNA, pre-miRNA, gene therapy, partially degraded RNA, transiently expressed RNA
Multiplex capability Up to 3-plex Single-plex
Detection Chromogenic or fluorescent Chromogenic FastRED
Sample type FFPE cells & tissues (TMAs)
Fixed frozen tissues
Fresh frozen tissues
Cultured cells
FFPE cells & tissues (TMAs)
Fresh frozen tissues
Pretreatment kit Reagent Kit includes Universal Pretreatment Kit Reagent kit includes Universal Pretreatment Kit
Kit RNAscope® kit* BaseScope kit*
Probe RNAscope® probe* BaseScope probe*
*RNAscope® and BaseScope Assay products components cannot be interchanged.