Name: Single-cell analysis with nanopore sequencing
Uploaded: 2023-10-23T00:00:00.0000000
Duration: T00H03M03S
Description: Single-cell analysis with nanopore sequencing

Name: Single-cell analysis with nanopore sequencing

Description: Single-cell analysis with nanopore sequencing

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Upload Date: 2023-10-23T00:00:00.0000000

Transcript: Language: EN.
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The tumor microenvironment is complex and continuously evolving as cancer cells grow and divide in an uncontrolled manner. Characterizing the transcriptome enables a deeper understanding of the pathways involved in tumor development and can reveal cancer associated gene expression changes. While bulk sequencing can identify specific variants associated with cancer growth, only information at the single cell level can determine which cell types are present and how they individually contribute.
Full length transcripts from single cells can be captured using a variety of methods. Nanopore sequencing protocols were validated using a 10x Genomics single cell preparation kit, which generates cDNA with unique cell barcodes and unique molecular identifiers. Traditional short read sequencing requires transcript fragmentation when generating single cell libraries.
This means that only a small region close to one end of a transcript is available for analysis. This limited representation of each transcript makes it difficult to quantify isoform level expression. Furthermore, as short reads are unlikely to span fusion junctions, fusion events are often missed. Nanopore sequencing, on the other hand, does not require fragmentation. Long nanopore reads can cover full length transcripts in single reads revealing novel fusion transcripts, complex structural variants, isoform diversity and splicing events.
Consequently, single cell whole transcriptome sequence analysis using long nanopore reads can : reveal unambiguous isoform changes, which could impact RNA regulation or protein function, providing novel insights into tumor heterogeneity; detect fusion transcripts, including simultaneous detection of single nucleotide variants and gene fusion events associated with cancer; and determine immune receptor sequences and isotypes to further understand the role of the immune system in cancer, which has the potential to provide new opportunities for immunotherapy.
To achieve the required depth of coverage for high-output, single-cell transcriptome analysis, Oxford Nanopore offers a range of PromethION sequencing devices with the ability to run from 1 to 48 flow cells. A single PromethION flow cell can generate around 80 million full length cell assigned reads, providing high-output and full-length transcripts for single cell analysis. To learn more about single-cell analysis with nanopore sequencing, check out our In Focus on the topic in association with Oxford Nanopore.

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