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Encore™ NGS Library Systems for Ion Torrent™
The Encore™ NGS Library Systems for Ion Torrent™ provide a simple, fast and scalable solution for producing DNA libraries used in a wide range of sequencing applications with the Ion Personal Genome Machine™ (PGM™) from Life Technologies. The streamlined workflow enables library construction with no need for specialized equipment to perform size selection. Starting from as little as 100 ng DNA, sequencing libraries can be created for genomic DNA/exome sequencing, amplicon sequencing, RNA-Seq, Digital Gene Expression (DGE), ChIP-Seq and more. The efficiency and cost of sequencing projects can be further optimized using either the Encore NGS Multiplex Library System I for Ion Torrent or the System IB for Ion Torrent, to enable up to 16-plex multiplex sequencing on the Ion Chip.
As shown in Figure 1, the workflow consists of four main steps: (1) Fragmented double-stranded DNA is size selected using an innovative, automation-friendly magnetic bead based procedure to isolate fragments with a median size of 150 base pairs (bp); (2) The ends of these fragments are repaired to generate blunt ends; (3) Adaptor molecules are ligated, placing specific adaptors on the 5' and 3' ends of each fragment; and (4) Fragments with ligated adaptors are generated by a fill-in reaction and simultaneous PCR amplification to produce the final library and allow for the optional incorporation of barcodes for multiplex sequencing. The entire workflow can be completed in four hours and yields DNA libraries ready for template preparation on the Ion PGM System. The Encore NGS Multiplex Library Systems for Ion Torrent use unique barcodes to facilitate sequencing of up to 16 samples on a single Ion Chip, thereby dramatically reducing the per sample cost and time required to obtain sequence data.
The Encore NGS Library Systems for Ion Torrent have been designed for seamless integration with both the Ovation® RNA-Seq System V2, Ovation RNA-Seq FFPE System and Ovation Prokaryotic RNA-Seq System to enable a complete end-to-end solution for transcriptome library construction using unfractionated total RNA samples.
Figure 2: Sequencing coverage with E. coli genomic DNA
Three independent sequencing libraries were constructed using 100 ng of E. coli genomic DNA using the Encore NGS Library System for Ion Torrent and sequenced on the PGM. The distribution of reads from each sample is plotted to determine the depth of coverage across the E. coli genome. The average number of total reads obtained for each sample was 566,000. 430,000 reads were randomly sub-sampled from each data set to generate the above plots. These experimental tracks are shown in red, gold, and green. The theoretical distribution based on randomly chosen sequences with lengths that emulate 430,000 reads from sample A is shown in blue.
Figure 3 shows the key technical matrices of a typical run using libraries generated with the Encore NGS Library Systems for Ion Torrent.