Next-generation sequencing

Biocenter Oulu Sequencing Center provides next-generation sequencing (NGS) for genomics and transcriptomics projects using two different platforms. The choice of the platform depends on the specific need of your project: what is the desired application, size of the project, research organism, desired sequencing depth and also other factors.

Sequencing platforms available:

Ion Torrent

Ion Torrent is fast small-scale NGS platform. It is suitable for small genome projects, gene expression analysis, targeted gene sequencing (captured and panels) and amplicon sequencing. There are three semiconductor chips available with different capacities 314, 316, and 318 and read lengths of 200, 400 and 500 bp (latter utilizing isothermal amplification chemistry). Typical throughputs for chips are:

Chip

Number of  Wells

Typical output

314

  1,2 M

100-150 Mbp

316

  6,3 M

0,7-1,2 Gbp

318

  11,3 M

up to 2,5 Gbp

We offer full sequencing service and also accept sequencing libraries prepared by our customers.  Sequencing is performed currently only using HiQ chemistry kit. DNA libraries are prepared using NebNext DNA library preparation kit, RNA libraries with Ion Total-RNA Seq v. 2.0 and panels with Ion Ampliseq Library Kit v. 2.0.  Customer amplicons can be purified, quantified and pooled from PCR reactions with automatic platform.

Person in charge: marko.suokas (at) oulu.fi

Illumina NextSeq550

NextSeq550 is high-throughput desktop sequencer, which enables flexible sequencing of exomes, targeted gene panels and transcriptomes in a single run with high data quality. For more information about the system, please visit the Illumina website.

NextSeq550 has two flow cell configurations with following sequencing performance:

Flow Cell Configuration

Read Length (bp)

      Output (Gb)

High Output Flow Cell

     2 x 150

          100-120

Up to 400 M single reads

     2 x 75

          50-60

Up to 800 M paired-end reads

     1 x 75

          25-30

Mid Output Flow Cell

     2 x 150

          32-39

Up to 130 M single reads

     2 x 75

          16-19

Up to 260 M paired-end reads

 

 

NextSeq550 enables also array scanning for following chips:

Infinium CytoSNP-850K BeadChip

HumanCytoSNP-12 BeadChip

Infinium HumanKaryomap-12 BeadChip 

Currently, we accept sequencing libraries prepared by the customers, and provide library preparation for exome sequencing and targeted gene panels.

Person in charge: katri.pylkas (at) oulu.fi

To get started with your NGS project

We offer help in experiment planning and in selection of the most suitable platform.

As number of parameters vary for a sequencing run (type of application, starting material, number of reads, number of samples to be pooled etc.), all new NGS experiments are started by arranging a project initiation meeting. In the initiation meeting all aspects of the project are discussed, including data analysis issues, to assist the researcher in designing the experiment to ensure the optimal experiment setup and sample preparation. Also the cost and schedule estimates are provided in these meetings.

Please contact us by e-mail ngs (at) oulu.fi and fill and attach the NGS Project Request Form to your mail. We will contact you as soon as possible.

Useful links:

https://www.illumina.com/library-prep-array-kit-selector.html

http://support.illumina.com/downloads/sequencing_coverage_calculator.html

http://www.illumina.com/landing/ngs-methods-guide.html

Last updated: 3.11.2016