Journal
NANO TODAY
Volume 46, Issue -, Pages -Publisher
ELSEVIER SCI LTD
DOI: 10.1016/j.nantod.2022.101596
Keywords
Single-cell sequencing; Digital microfluidics; Multi-omics sequencing; Multiple myeloma
Categories
Funding
- National Natural Science Foundation of China [21927806, 22104080]
- Fundamental Research Funds for the Central Universities [20720210001]
- Innovative Research Team of High -Level Local Universities in Shanghai [SSMU- ZLCX20180701]
- National Science Fund for Fostering Talents in Basic Science (NFFTBS) [J1310024]
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This article introduces a nanoliter-scale single-cell multi-omics sample preparation platform called DMF-DR-seq, based on digital microfluidics. DMF-DR-seq demonstrates improved performance compared to current technology, with lower amplification bias, higher genome-wide coverage in DNA sequencing, and better gene detection ability in RNA sequencing. DMF-DR-seq was used to identify genome variation-induced abnormal transcriptome expression, revealing potential essential genes involved in the pathologic progress. The unique flexibility, sensitivity, and accuracy of DMF-DR-seq suggest its potential utility in deeper multi-omics analysis for inheritance mechanism study in single-cell biology.
Single-cell genome and transcriptome sequencing investigates how genotype influences the phenotype of single cells, so as to comprehensively interpret biological inheritance and explain functional heterogeneity at the single-cell level. Current sample preparation technologies for simultaneous DNA and RNA sequencing of the same cell are cumbersome, expensive, and suffer from cross-contamination and limited sensitivity. Herein we describe DMF-DR-seq, a nanoliter-scale single-cell multi-omics sample preparation platform based on digital microfluidics. DMF-DR-seq integrates the major steps of single-cell isolation, DNA/RNA separation, and nucleic acid amplification in situ. The results confirm the enhanced ability of DMF-DR-seq relative to current state-of-the-art technology, with lower amplification bias, higher genome-wide coverage in DNA sequencing and better gene detection ability in RNA sequencing results. By using DMF-DR-seq, we identified the genome variation-induced abnormal transcriptome expression of single circulating tumor cells (CTCs) and cancer cells from multiple myeloma patients. The results identified potentially essential genes, known as transporters associated with antigen presentation (TAP1 and TAP2), that participate in the pathologic progress. The unique flexibility, sensitivity, and accuracy of DMF-DR-seq suggest its potential utility in deeper multi-omics analysis for inheritance mechanism study in single-cell biology.(c) 2022 Elsevier Ltd. All rights reserved.
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