Visualize a specific RNA locus at single cell sensitivity with spatial and morphological context

The BaseScope Assay is a unique product from ACD, based on the same platform of proven and established RNAscope™ technology that has been cited in over 8,000 publications in over 10 years. This powerful assay provides new data dimensions and unique insight into biological mechanisms. The BaseScope Assay enables applications such as the detection of exon junctions/splice variants, short/highly homologous RNA sequences (50-300 bases), and point mutations at single cell sensitivity.

  • Detecting biological events in cells and in situ using a single Z pair
  • Highly specific and sensitive detection of RNA targets with down to ONE nucleotide differences
  • Analysis of broad sample types: FFPE cells & tissues (TMAs), Fresh or fixed frozen tissues, Cultured cells
Exon Junctions / Splice VariantsShort SequencesPoint Mutations
 Gene therapy/AAV 
Exon Junctions / splice variantsShort / highly homologous gene sequences (50-300nt)Point Mutations (ACD validated point mutations only)
Circular RNA (circRNA)T cell receptors (TCRs) and CDR sequences in T-cell clonesShort InDel
Gene fusionGene editing / CRISPRHomologous
Gene knockout (KO)Pre-miRNA 

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

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


“We have had a fantastic experience using BaseScope as an integral part of our ongoing genomics research. The procedure is straightforward and robust, providing meaningful data to support novel genomic observations that couldn't be easily obtained in another fashion. Most importantly, working with ACD has been exceedingly beneficial. They act as collaborators, consistently communicating with us to ensure we have what we need while displaying a willingness to work with us to advance our science.” 

Ming-Hsiang Lee, Ph.D. and Carter Palmer (Ph.D. Candidate)
The Chun Lab
Sanford Burnham Prebys Medical Discovery Institute

Recent publication: Nature. 2018 Nov 21. PMID: 30464338


Major applications for the BaseScope™ assay include gene editing and highly homologous short targets.

Visualization of in vivo gene editing heterogeneity at the transcript level with the BaseScope™ Duplex RNA in situ hybridization assay

BaseScope™ Probes for MAGEA Gene Family Detection

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Enabling researchers to publish single-cell resolution data with the BaseScope™ assay in major journals.

BaseScope™ Publication List

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Advanced Cell Diagnostics

Our new headquarters office starting May 2016:

7707 Gateway Blvd.  
Newark, CA 94560
Toll Free: 1 (877) 576-3636
Phone: (510) 576-8800
Fax: (510) 576-8798



19 Barton Lane  
Abingdon Science Park
OX14 3NB
United Kingdom
Phone 2: +44 1235 529449
Fax: +44 1235 533420



Advanced Cell Diagnostics China

Unit 1901, Tower 3,
Raffles City Changning Office,
1193 Changning Road, Shanghai 200051


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