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FocuSCOPE® – Detect Transcriptome and Variants in Single Cells

Focus on genes that matter! The FocuSCOPE® Single Cell Targeted Capture Kit utilizes targeted customized probes for simultaneous whole transcriptome sequencing and detection of mutations, gene fusions, and viral sequences from the same single cells.

Kit Highlights

The core technology of FocuSCOPE® is centered around specially designed Barcoding Beads with both customizable probes and poly-T probes that capture poly-adenylated mRNA and your specific transcripts of interest. During the workflow, cDNA is split, and two different libraries are prepared which can be combined for sequencing.

Enrich target region + whole transcriptome from the same single cells
Capture up to 10 self-defined target regions at single cell level
Suitable for SNVs, Fusion genes, viral sequences and more
Ready-to-Use Pre-Validated Panels

Performance Data

Acute Promyelocytic Leukemia: PML-RARA3 Fusion Gene Detection at Single Cell Level

A xenografted tumor model, derived from the NB4 cell line harboring the PML-RARA fusion gene t (15;17), was utilized. Clustering data unveiled a notably elevated detection rate of the PML-RARA fusion gene in libraries constructed with our targeted FocuSCOPE beads in combination with poly(dT) probes, compared to libraries constructed with poly(dT) probes alone. Data show increased PML-RARA fusion gene detection rate using FocuSCOPE targeted probes.

High Epstein-Barr Virus (EBV) Detection Rate with Targeted Probes

The Raji cell line, which carries the latent Epstein-Barr Virus, was employed alongside A549 cell lines as a control. Libraries were prepared using either FocuSCOPE® EBV beads (comprising EBV-targeted probes and poly(dT) probes) or beads with poly(dT) probes alone. Sequencing data revealed a higher detection rate for EBV in the group utilizing our FocuSCOPE® EBV beads.

High SNV Detection in Xenograft model of R248Q-mutated TP53

In this cell-line-derived xenograft (CDX) tumor model, NB4 cells, a cell line harboring a single nucleotide variant of TP53 (R248Q) and the PML-RARA fusion gene was subcutaneously injected into immunodeficient mice. Libraries were generated using FocuSCOPE Custom Tag Barcoding Beads or poly-T beads. Sequencing data revealed a higher detection rate for the SNV of TP53 in the group utilizing our FocuSCOPE® SNV beads.

Streamlined workflow: from sample to two libraries within one workday


Single Cell Suspension

Cell Partitioning, Lysis & Barcoding

Whole Transcriptome Library and Targeted Library Generation


Bioinformatics Analysis

Applications Areas

Technical Specifications

Up to 10 target regions

fully customizable (up to 200bp target region) | pre-validated panels (Blood cancer, CHIP, EBV and lung cancer)

30 000 cells

choose between SD and HD chip depending on required capture rate


Full instruments-free workflow


PythoN: tissue dissociation
NEO: single cell processing

Targeted Variant Detection Pre-Validated Panels

Blood Cancer Panel


Lung Cancer Panel


Clonal Hematopoiesis Panel






Two libraries are generated (whole transcriptome + enrichment library).

Beads consist of both PolyT and target probes. There is a tradeoff. We recommend not going more than 10 to sufficiently capture the whole transcriptome.

For FocuSCOPE, we recommend Paired-End (PE) 150. Sequencing Depth: 20,000 – 50,000 read pairs per cell for the whole transcriptome library and 5,000 reads per cell for the enrichment library.

Yes, it can detect deletions.

The length of our probes is ~25-30 bases.

The kit is suitable for human PBMC and bone marrow.

It is possible to use cryopreserved cells.

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