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Confidently Resolve Cellular Heterogeneity

Differences in isoform expression and relative abundance among individual cells can be an important clue in understanding how populations of cells interact to function as a complex system. Whether you are exploring the immune system, the brain, or tumor environment, only highly accurate long reads (HiFi reads) can provide unbiased, direct detection of isoforms in your single-cell study.

Resolve isoform diversity at the single-cell level

HiFi reads deliver the high accuracy and long reads needed to capture intact isoform information without assembly or complicated algorithms, including at the single cell level. Single-cell RNA sequencing using the Iso-Seq method allows you to:

  • Generate full-length transcript isoforms that can be confidently assigned to individual cells
  • Move beyond 3’ gene counting to include TSS, polyA, and complete exon connectivity data to deepen your understanding of cell type differences
  • Distinguish cell types that play unique roles in complex systems like the immune system
  • Understand how alternative splicing of critical genes drives function in tissues like the brain

Workflow: From RNA to full-length transcripts at a single-cell level

 

Sample & Library Preparation
Prepare full-length transcripts from single-cell RNA preparations using your preferred platform

Learn More


Sequencing
Simplify sample prep workflow and reduce project costs by using the Sequel Systems

Learn More


Data Analysis
Identify, classify, and filter full-length isoforms at the single-cell level

Learn More


 

 

Application Brief: Learn more about these best practices for single-cell RNA sequencing

 

 


 

Spotlight: HIT-scISOseq enables high throughput, high accuracy, single-cell sequencing of full-length transcripts

HIT-scISOseq yields >10 million high-accuracy full-length isoforms in a single SMRT Cell 8M on the Sequel II System for high-throughput single-cell isoform sequencing. By combining full-length cDNA capture with biotinylated PCR primers and a novel head-to-tail concatenation step, HIT-scISOseq provides eight times more data output than the standard single-cell RNA sequencing protocol.

Zheng, Y.-F., et al. (2020) HIT-scISOseq: High-throughput and high-accuracy single-cell full-length isoform sequencing for corneal epithelium. bioRxiv Preprint.

Spotlight: Gene-wise comparisons reveal more differences between mouse neuronal cell types than exon pairwise comparisons

Using full-length isoform information, including transcription start site (TSS) and polyA data, 395 genes show significantly different expression in the hippocampus versus prefrontal cortex cells, whereas only 31 genes met the same criteria using short-read data. In the above figure, a 6nt microexon in Nsfl1c (orange) is preferentially expressed in the hippocampus across neuronal and glial cell types but is absent in the same pre-frontal cortex cell types.

Joglekar, A., et al. (2020) Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development. bioRxiv Preprint.

To learn more about how to use single-cell RNA sequencing in your research, contact us.