nuc-seq/SNES
Single G2/M Nucleus Sequencing of Cells in S Phase/Single Nucleus Exome Sequencing
A modified MDA protocol, nuc-seq takes advantage of the fact that a single cell in the G2_M stage of the cell cycle has 4 copies of the genome. This property allows the cells to be isolated with a cell sorter, and it also significantly increases the genome coverage of single cells (Wang et al., 2014). SNES is an additional variation that includes targeted selection and sequencing of the exomes (Leung et al., 2015). Div-Seq is a variation that combines nuc-seq with pulse labeling of proliferating cells by 5-ethynyl-2_-deoxyuridine (EdU) Habib et al., 2016)
Advantages:
- nuc-seq: Improves physical coverage performance to more than 90% for single-cell sequencing
- SNES: 95.94% exome coverage in single cells
- SNES: Detection efficiencies of 92.37% for SNVs in an isogenic population
Disadvantages:
- nuc-seq: Cannot be applied to cells with low proliferation rates
- SNES: Limited to exomes
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Zhang X., Marjani S. L., Hu Z., Weissman S. M., Pan X., et al. Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects. Cancer Res. 2016;76:1305-1312
Leung M. L., Wang Y., Waters J. and Navin N. E. SNES: single nucleus exome sequencing. Genome Biol. 2015;16:55
Saadatpour A., Lai S., Guo G. and Yuan G. C. Single-Cell Analysis in Cancer Genomics. Trends Genet. 2015;31:576-586
Szulwach K. E., Chen P., Wang X., et al. Single-Cell Genetic Analysis Using Automated Microfluidics to Resolve Somatic Mosaicism. PLoS One. 2015;10:e0135007
Voet T. and Van Loo P. SNES makes sense? Single-cell exome sequencing evolves. Genome Biol. 2015;16:86
Wang Y. and Navin N. E. Advances and applications of single-cell sequencing technologies. Mol Cell. 2015;58:598-609
References:
Leung M. L., Wang Y., Waters J. and Navin N. E. SNES: single nucleus exome sequencing. Genome Biol. 2015;16:55
Leung M. L., Wang Y., Kim C., Gao R., Jiang J., et al. Highly multiplexed targeted DNA sequencing from single nuclei. Nat Protoc. 2016;11:214-235
Habib N., Li Y., Heidenreich M., et al. Div-Seq: A single nucleus RNA-Seq method reveals dynamics of rare adult newborn neurons in the CNS. bioRxiv. 2016;
Related
History: nuc-seq/SNES
Revision by on 2017-06-21 07:50:24 - Show/Hide
Single G2/M Nucleus Sequencing of Cells in S Phase/Single Nucleus Exome Sequencing
A modified MDA protocol, nuc-seq takes advantage of the fact that a single cell in the G2_M stage of the cell cycle has 4 copies of the genome. This property allows the cells to be isolated with a cell sorter, and it also significantly increases the genome coverage of single cells (Wang et al., 2014). SNES is an additional variation that includes targeted selection and sequencing of the exomes (Leung et al., 2015). Div-Seq is a variation that combines nuc-seq with pulse labeling of proliferating cells by 5-ethynyl-2_-deoxyuridine (EdU) Habib et al., 2016)
Advantages:- nuc-seq: Improves physical coverage performance to more than 90% for single-cell sequencing
- SNES: 95.94% exome coverage in single cells
- SNES: Detection efficiencies of 92.37% for SNVs in an isogenic population
Disadvantages:- nuc-seq: Cannot be applied to cells with low proliferation rates
- SNES: Limited to exomes
Reagents:Illumina Library prep and Array Kit SelectorReviews:Zhang X., Marjani S. L., Hu Z., Weissman S. M., Pan X., et al. Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects. Cancer Res. 2016;76:1305-1312Leung M. L., Wang Y., Waters J. and Navin N. E. SNES: single nucleus exome sequencing. Genome Biol. 2015;16:55Saadatpour A., Lai S., Guo G. and Yuan G. C. Single-Cell Analysis in Cancer Genomics. Trends Genet. 2015;31:576-586Szulwach K. E., Chen P., Wang X., et al. Single-Cell Genetic Analysis Using Automated Microfluidics to Resolve Somatic Mosaicism. PLoS One. 2015;10:e0135007Voet T. and Van Loo P. SNES makes sense? Single-cell exome sequencing evolves. Genome Biol. 2015;16:86Wang Y. and Navin N. E. Advances and applications of single-cell sequencing technologies. Mol Cell. 2015;58:598-609References:Leung M. L., Wang Y., Waters J. and Navin N. E. SNES: single nucleus exome sequencing. Genome Biol. 2015;16:55Leung M. L., Wang Y., Kim C., Gao R., Jiang J., et al. Highly multiplexed targeted DNA sequencing from single nuclei. Nat Protoc. 2016;11:214-235Habib N., Li Y., Heidenreich M., et al. Div-Seq: A single nucleus RNA-Seq method reveals dynamics of rare adult newborn neurons in the CNS. bioRxiv. 2016;Revision by sbrumpton on 2017-06-21 07:50:21 - Show/Hide
Single G2/M Nucleus Sequencing of Cells in S Phase/Single Nucleus Exome Sequencing
A modified MDA protocol, nuc-seq takes advantage of the fact that a single cell in the G2_M stage of the cell cycle has 4 copies of the genome. This property allows the cells to be isolated with a cell sorter, and it also significantly increases the genome coverage of single cells (Wang et al., 2014). SNES is an additional variation that includes targeted selection and sequencing of the exomes (Leung et al., 2015). Div-Seq is a variation that combines nuc-seq with pulse labeling of proliferating cells by 5-ethynyl-2_-deoxyuridine (EdU) Habib et al., 2016)
Advantages:- nuc-seq: Improves physical coverage performance to more than 90% for single-cell sequencing
- SNES: 95.94% exome coverage in single cells
- SNES: Detection efficiencies of 92.37% for SNVs in an isogenic population
Disadvantages:- nuc-seq: Cannot be applied to cells with low proliferation rates
- SNES: Limited to exomes
Reagents:Illumina Library prep and Array Kit SelectorReviews:Zhang X., Marjani S. L., Hu Z., Weissman S. M., Pan X., et al. Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects. Cancer Res. 2016;76:1305-1312Leung M. L., Wang Y., Waters J. and Navin N. E. SNES: single nucleus exome sequencing. Genome Biol. 2015;16:55Saadatpour A., Lai S., Guo G. and Yuan G. C. Single-Cell Analysis in Cancer Genomics. Trends Genet. 2015;31:576-586Szulwach K. E., Chen P., Wang X., et al. Single-Cell Genetic Analysis Using Automated Microfluidics to Resolve Somatic Mosaicism. PLoS One. 2015;10:e0135007Voet T. and Van Loo P. SNES makes sense? Single-cell exome sequencing evolves. Genome Biol. 2015;16:86Wang Y. and Navin N. E. Advances and applications of single-cell sequencing technologies. Mol Cell. 2015;58:598-609References:Leung M. L., Wang Y., Waters J. and Navin N. E. SNES: single nucleus exome sequencing. Genome Biol. 2015;16:55Leung M. L., Wang Y., Kim C., Gao R., Jiang J., et al. Highly multiplexed targeted DNA sequencing from single nuclei. Nat Protoc. 2016;11:214-235Habib N., Li Y., Heidenreich M., et al. Div-Seq: A single nucleus RNA-Seq method reveals dynamics of rare adult newborn neurons in the CNS. bioRxiv. 2016;