Single-cell RNA sequencing

Full-length isoform information for your single-cell transcriptome studies

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Reveal hidden isoform diversity at single-cell resolution

Understanding cell heterogeneity at the isoform level is critical for basic and disease research. Short reads can only capture gene-level information, while other long-read technologies lack the accuracy for accurate UMI/barcode identification.

Only HiFi reads can provide accurate detection of isoforms in your single-cell study. No complicated algorithms for barcode correction or orthogonal sequencing data are required.

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With the MAS-Seq for 10x Single Cell 3′ kit, you can:

  • Achieve 16-fold throughput increase in Sequel II/IIe and Revio systems
  • Move from gene counting to full-length isoform information
  • Reveal cell type-specific spliced isoforms and expressed variants

Connect with a PacBio scientist

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Video Webinar

Single-cell RNA sequencing with MAS-Seq. When genes are not enough

During this engaging webinar, PacBio scientists present the MAS-Seq method, an all-new kitted single-cell transcriptomics solution that delivers unmatched data quality and explanatory power for your next big breakthrough discovery! Hear why isoforms, not genes, are critical for single-cell research. See how highly accurate, full-length isoform information at the single-cell level using the MAS-Seq method can deliver groundbreaking insights into disease biology. And finally, learn how to easily integrate MAS-Seq into your single-cell studies to discover hidden isoform diversity with a library prep walk-through and user-friendly informatics workflows.



Single-cell reads

Long-read sequencing performance
Short reads Other long reads PacBio
Single technology X
Isoform information X
Variant information X
Official software X

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Video Tutorial

MAS-Seq for Single Cell Bioinformatics Walkthrough

The PacBio MAS-Seq for 10x Single Cell 3’ kit provides a 16-fold throughput increase on PacBio’s sequencing systems, enabling isoform resolution for single-cell transcriptomics. In this tutorial, we demonstrate how to use PacBio’s SMRT Link software to analyze MAS-Seq single cell data to produce gene- and isoform-level count matrices that can be used with tertiary analysis tools such as Kana, Seurat, and CellTypist for cell clustering and cell labeling.

For more information on PacBio single-cell isoform informatics, visit

Tech note


The Jumpcode Single Cell RNA Boost kit is compatible with PacBio’s MAS-Seq for 10x Single Cell 3’ kit. Using CRISPR-Cas9 technology targeting uninformative genes that are ignored by single-cell analysis, boosting discovery power of rare isoforms and cell types that otherwise cannot be seen.




Image of a graph showing percentage aligned reads vs. Mas-Seq and Mas-Seq + CRISPRclean

Common questions about single-cell RNA sequencing and the MAS-Seq kit

Single-cell RNA sequencing (scRNA-seq) emerged to characterize gene expression differences between individual cells derived from a complex tissue, allowing a higher-resolution look at the transcriptome. A typical single-cell library takes RNA as input and outputs cDNA molecules that have been tagged with single-cell barcodes and unique molecular indices (UMIs) so that transcripts can be traced back to their “single cell” origins. This is in contrast with, bulk RNA-Seq, where there are no single-cell barcodes to attribute transcripts back to cells.

Single-cell RNA sequencing using PacBio HiFi reads offers full-length isoform information at the single-cell level. Short-read sequencing only sequences a short fragment of one end of the transcript, providing only gene-level information. In contrast, PacBio HiFi reads can cover the entire transcript, revealing isoform diversity at the single-cell level. Isoforms — not genes — are often the driver of disease and biology.

The MAS-Seq method was developed by Al’Khafaji et al. as a concatenation method for increasing throughput by joining cDNA molecules generated from single-cell platforms into longer concatenated fragments. HiFi reads generated from sequencing the concatenated molecules can then be bioinformatically broken up to retrieve the original molecules. The result is higher throughput and reduced sequencing needs. The authors showed that, applying the MAS-Seq method to 10x single-cell libraries, unique isoforms associated with specific cell types relevant to cancer can be distinguished which are otherwise undetectable using short-read single-cell RNA-Seq.


Yes! With MAS-Seq, you can obtain full-length isoform information for your single-cell libraries, whereas with other sequencing methods, such as short reads, you can only obtain gene-level information. Multiple publications, using MAS-Seq (Al’Khafaji et al.) or regular HiFi sequencing (Palmer et al., Joglekar et al.) have demonstrated the use of PacBio for identifying cell-type isoform specificity.

No. With the MAS-Seq kit, PacBio HiFi sequencing offers sufficient coverage for a typical single-cell experiment with 1 SMRT Cell on the PacBio long-read systems. No orthogonal sequencing technology is required.

The MAS-Seq kit is compatible with cDNA generated using the 10x Chromium Next GEM Single Cell 3’ kit (v3.1).

The MAS-Seq kit is compatible with Sequel II/IIe and Revio systems.

The SMRT Link Read Segmentation & Single-cell Iso-Seq workflow processed MAS-Seq data to produce gene- and isoform-count matrix data that is compatible with common tertiary analysis tools such as Seurat. Further bioinformatics information can be found at

Single-cell transcriptomics for cancer research

A more complete transcriptome for cancer research – now at single-cell level. With MAS-Seq, upgrade your single-cell cancer research to:

  • Discover isoforms as potential biomarkers and help enable therapeutic targets
  • Identify fusion isoforms
  • Detect expression mutations

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Empower your single-cell transcriptome study with MAS-Seq

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