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Next generation sequencing

The Applied Biosystems SOLiD™ 3 System is a revolutionary genetic analysis platform that enables massively parallel sequencing of clonally-amplified DNA fragments linked to beads. The sequencing methodology is based on sequential ligation with dye-labelled oligonucleotides. This technology provides unmatched accuracy, ultra-high throughput and application flexibility to advance your research.

How it works

Start with a fragment or mate-paired library depending on the application and information needed. Prepare clonal bead populations in microreactors containing template, PCR reaction components, beads and primers. After PCR, denature the templates and perform a bead enrichment step to separate beads with extended templates from undesired beads. Then deposit the 3’ modified beads onto a glass slide. Once loaded onto the Analyzer, primers hybridize to the adapter sequence within the library template. A set of four fluorescently labelled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length. Following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles. Five rounds of primer reset are completed for each sequence tag. For mate-paired libraries, the entire process is repeated.

Applications

Whole Transcriptome Analysis.

SOLiD 3 System

The SOLiD 3 System provides researchers with access to the entire transcriptome with a hypothesis generating, highly sensitive assay that preserves the strand information of the original RNA molecule. The combination of 1 billion sequence tags and sample multiplexing capabilities allow cost effective analysis of multiple samples in a single run while maintaining the sensitivity to discover molecules present at low levels.

Whole Genome Resequencing.

The SOLiD 3 System enables a new level of whole genome sequencing with massive throughput and mate-paired technology. The system’s ultra high throughput results in high coverage levels and the ability to sequence multiple genomes in a single run. The combination of unmatched throughput and superior accuracy dramatically reduces the time and cost to lower than that of other technologies.

Targeted resequencing.

The superior accuracy of the SOLiD 3 System provides a very low false positive rate that enables variation detection with less coverage than alternative platforms. The inclusion of barcodes for sample multiplexing dramatically lowers the cost, time and labour involved in processing multiple samples.

Small RNA analysis.

The SOLiD Small RNA Solution is a robust method for hypothesis-generating, whole genome analysis of expression patterns that enable discovery of novel RNA without the probe bias of microarrays. Using the SOLiD Small RNA Expression Kit, you can convert total RNA into a library suitable for emulsion PCR using five easy steps with a single purification. This simplified protocol conserves the strand information of the original molecule and enables one to decipher strand-specific expression patterns.

Chromatin Immunoprecipitation (ChIP).

ChIP-Sequencing (ChIP-Seq) with the SOLiD 3 System combines a chromatin immunoprecipitation (ChIP) assay with massively parallel DNA sequencing, offering a highly sensitive method to accurately characterize the protein-DNA interactions of an entire genome. Additionally, the SOLiD System’s flexible slide format and multiplexing capability allows researchers to analyze multiple samples in a single run.

Methylation Analysis.

The SOLiD 3 System provides a high throughput method for analyzing genome-wide DNA methylation with a much higher level of resolution than traditional methods.

Curator: Dr Paul Smyth

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Last updated 21 September 2016 Paul Smyth (Email).