BioMicroCenter:Nextera: Difference between revisions
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Nextera DNA sample preparation, from Epicentre technologies, uses a modified transposase to simultaneously fragment intact genomic DNA and tag it with Illumina adapters. A limited number of PCR steps are required to generate complete Illumina libraries. | [[Image:I_Nextera_Illumina_fig1.gif|right]]Nextera DNA sample preparation, from Epicentre technologies, uses a modified transposase to simultaneously fragment intact genomic DNA and tag it with Illumina adapters. A limited number of PCR steps are required to generate complete Illumina libraries. | ||
[[Image:Nextera_2.png|center|550px|left]]Nextera-prepared samples provided a similar quality of sequencing data compared with samples prepped in parallel on the SPRI-Works system. DNA from the same Colobacter sample was either sonicated for SPRI-prep or provided as intact DNA for Nextera prep. The samples were multiplexed and sequenced together on an Illumina GAII 40bp single-end lane. The total genomic coverage for both Nextera and SPRI-te samples was exactly the same at 97.8% coverage of Colobacter’s GC-rich genome, although complexity was greater in the sonicated samples. | |||
The Nextera transposase does exhibit a mild GC-insertion bias, shown by the increase in percent of the first few bases. This, however, did not affect the sequencing coverage. The Nextera-prepared sample has very consistent genome-wide coverage, while the SPRI-prepared samples have a more variable coverage density. | The Nextera transposase does exhibit a mild GC-insertion bias, shown by the increase in percent of the first few bases. This, however, did not affect the sequencing coverage. The Nextera-prepared sample has very consistent genome-wide coverage, while the SPRI-prepared samples have a more variable coverage density. | ||
Revision as of 09:15, 29 September 2011
Nextera DNA sample preparation, from Epicentre technologies, uses a modified transposase to simultaneously fragment intact genomic DNA and tag it with Illumina adapters. A limited number of PCR steps are required to generate complete Illumina libraries.
Nextera-prepared samples provided a similar quality of sequencing data compared with samples prepped in parallel on the SPRI-Works system. DNA from the same Colobacter sample was either sonicated for SPRI-prep or provided as intact DNA for Nextera prep. The samples were multiplexed and sequenced together on an Illumina GAII 40bp single-end lane. The total genomic coverage for both Nextera and SPRI-te samples was exactly the same at 97.8% coverage of Colobacter’s GC-rich genome, although complexity was greater in the sonicated samples.
The Nextera transposase does exhibit a mild GC-insertion bias, shown by the increase in percent of the first few bases. This, however, did not affect the sequencing coverage. The Nextera-prepared sample has very consistent genome-wide coverage, while the SPRI-prepared samples have a more variable coverage density.
We have used Nextera DNA sample preparation for multiple samples and have seen high-quality data for all the samples. Below is an example of a CNV study prepared with Nextera DNA preparation.
