BASESCOPE™

VISUALIZE A SPECIFIC RNA LOCUS AT SINGLE CELL RESOLUTION • Gain insights on tissues by linking single-cell data with spatial and morphological context! Unlike existing techniques such as PCR

or NGS, imagine the ability to preserve spatial and morphological information at cellular resolution.

• Experience a whole NEW ERA of SPATIAL GENOMICS! Envision the detection of splice variant, short/highly homologous gene, and point mutation at single cell resolution.

• The revolutionary BaseScopeTM technology enables highly specific and sensitive detection and VISUALIZATION of RNA targets with down to ONE nucleotide differences, IN SITU, with SPATIAL MAPPING and MORPHOLOGICAL CONTEXT, under a brightfield light microscope.

EXON JUNCTION/SPLICE VARIANT DETECTION

Supporting research of genome-wide splicing events and understanding functionality of those variants

APPLICATIONS:

• Exon junctions/splice variants

• Circular RNA (circRNA)

• Gene fusion

• Gene knockout (KO)

SPLICE VARIANT EXAMPLE: Detection of exon 14 skipped variant of MET mRNA (MET ∆14) in lung cancer cell line.

E13/15 probe E14/15 probe

SHORT TARGET SEQUENCE DETECTION

Supporting growing research on short or highly homologous markers by monitoring gene expression in situ

APPLICATIONS:

• Short targets/highly homologous gene sequences (50-300nt)

• T-cell receptors (TCRs) and CDR sequences in T-cell clones

• Gene editing/CRISPR

• Pre-miRNA

The probe for exon junctions 13/15 detected expression of METΔ14 only in the H596 cell line. The probe for exon junctions 14/15 did not detect expression of wild-type MET in the H596 cell line.

EXAMPLE OF MET mRNA PROBE DESIGN:

MET∆14 E12

E13/15 probe

E13 E15

E14/15 probe

E12 E13 E14 E15MET WT

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GENE EDITING EXAMPLE: Specific and sensitive duplex detection to discern monoallelic or biallelic gene-editing status of cells in CRISPR/Cas9-treated liver tissues.

Vehicle CRISPR /Cas9

WT-only hepatocytes

Edited-only hepatocytes

Co-expressing hepatocytes

The WT sequence (green) was detected in unedited liver (vehicle) and the Edited liver (CRISPR/Cas9), whereas the Edited sequence (red) was detected only in the Edited liver (CRISPR/Cas9). Most hepatocytes expressed either WT only or Edited only, however a few cells co-expressed both the WTW and Edited sequences.

POINT MUTATION DETECTION

Supporting research of genetic mutations at down to a single nucleotide alteration

APPLICATIONS:

• Point mutation

• Short Insertions/Deletions

• Homologues

POINT MUTATION EXAMPLE: Detection of KRAS G12D in KRAS mutant and wild type cell lines.

The probe specific for mutant KRAS-G12D was detected only in the SNU-C2B cell line and not in the Hut78 cell line.

ACD Validated Point Mutations Only.

To see a list of ACD Validated Point Mutations, please visit acdbio.com/science/applications/ research-areas/point- mutation

KRAS G12D (+) cell line KRAS G12D (-) cell line

Be the first to spatially map splice variants, short/highly homologous genes, and point mutations at single cell resolution in the tissue context with the BaseScopeTM assay.

BaseScopeTM assays are available for both manual or automated platforms.

Learn more | acdbio.com

https://acdbio.com/science/applications/research-areas/point-mutation https://acdbio.com/science/applications/research-areas/point-mutation http://www.acdbio.com