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Concurrent Single-Cell RNA and Targeted DNA Sequencing for Genomic and Transcriptomic Signatures

Multiomics

Say Li Kong, Huipeng Li, Joyce A. Tai, Elise T. Courtois, Huay Mei Poh
Translational Research and Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore
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(...) Published on Rev A

  • supported ifcs:
    Open App IFC
  • number of ifc runs:
    5

Overview

A new multi-omic approach enabling concurrent measurement of full-length mRNA and targeted genomic DNA from the same single cell. CORTAD Seq offers an unbiased and flexible approach for single-cell multi-omic analysis. As described recently in Clinical Chemistry, C1 Open App IFCs are used to generate high-quality RNA sequencing data with good coverage of the targeted genomic loci, which is essential for accurate detection of single-nucleotide variations, deletion mutations, copy number variation and haplotype construction.

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Protocol: CORTAD Seq v1Duration (H:M): 1:00

Cell Load and Stain

Sample Prep

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Tested Primary Cells or Cell Lines

Cell Name Cell Type Source
PC9 Lung cancer Cell line

Performance

As proof of principle, we applied CORTADseq to lung cancer cell lines to dissect the cellular consequences of mutations that result in resistance to targeted therapy. We obtained a mean detection of 6000 expressed genes and an exonic rate of 50%. The targeted DNA-sequencing data achieved a 97.8% detection rate for mutations and allowed for the identification of copy number variations and haplotype construction. We detected expression signatures of tyrosine kinase inhibitor (TKI) resistance, epidermal growth factor receptor (EGFR) amplification, and expansion of the T790M mutation among resistant cells. We also identified characteristics for TKI resistance that were independent of EGFR T790M, indicating that other alterations are required for resistance in this context.

Publications or Articles

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Performance data

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