Genomic and transcriptomic sequencing

RNA-Seq, transcriptome

  • Transcriptome sequencing (total RNA and mRNA) with Illumina’s NextSeq550
  • Libraries are prepared with strand specific kits (Illumina). The amount of samples per run depends on the application (usually 10 to 40 samples).
  • The total RNA concentration and quality is checked before preparation of the libraries for sequencing
  • The service includes initiation meeting with the customer
  • Data is delivered in FASTQ format
  • Additional services include assistance in data analysis
  • Instructions how to prepare your RNA samples can be found here
  • Contact: katri.pylkas (at) oulu.fi, ngs (at) oulu.fi

RNA-Seq, small RNA sequencing

  • Small RNA sequencing and small-scale transciptome sequencing with Ion Torrent
  • Libraries are prepared with Ion Total-RNA Seq v. 2.0 kit from Thermo Scientific
  • The total RNA concentration and quality is checked before preparation of the RNA libraries for sequencing
  • The service includes initiation meeting with the customer
  • Data is delivered in FASTQ format
  • Additional services: assistance in Data analysis
  • Contact: marko.suokas (at) oulu.fi, ngs (at) oulu.fi

Exome sequencing

  • DNA samples are sequenced  up to 12 sample batches with Illumina NextSeq550 instrument
  • Customer delivers purified DNA samples, preparation instructions here
  • Total DNA concentration and quality is checked before preparation of the libraries for sequencing
  • The service includes initiation meeting with the customer
  • Data is delivered in FASTQ and aligned (h19) format
  • Additional services include assistance in data analysis
  • Contact: katri.pylkas (at) oulu.fi, ngs (at) oulu.fi

Gene panel sequencing with NextSeq550

  • Libraries can be prepared for various gene panels utilizing Nextera rapid capture chemistry
  • Customer delivers purified DNA samples, preparation instructions here
  • Total DNA concentration and quality is checked before preparation of the libraries for sequencing
  • The service includes initiation meeting with the customer
  • Data is delivered in FASTQ and aligned (h19) format (optional)
  • Additional services include assistance in data analysis
  • katri.pylkas (at) oulu.fi, ngs (at) oulu.fi

DNA/RNA Gene panel sequencing with Ion Torrent PGM

  • Library preparation of various gene panels utilizing Ion AmpliSeq technology   
  • The customer delivers purified nucleic acid samples
  • The concentration and quality is checked before preparation of the libraries for sequencing
  • The service includes initiation meeting with the customer
  • Data is delivered in FASTQ and optionally aligned format
  • Additional services: assistance in data analysis
  • Contact: marko.suokas (at) oulu.fi, ngs (at) oulu.fi

Amplicon sequencing with Ion Torrent PGM

  • DNA/RNA sequencing of amplicons (e.g. PCR products) with IonTorrent instrument (NGS) using HiQ assay kits
  • The total DNA/RNA concentration and purity is checked before sequencing
  • The amplicons (e.g. PCR products) are purified with Nugleomag automation robot
  • The purity and length of different amplicons are measured with MultiNA instrument
  • The service includes initiation meeting with the customer
  • Data is delivered in FASTQ format
  • Additional services: assistance in data analysis
  • Contact: marko.suokas (at) oulu.fi, ngs (at) oulu.fi

Sequencing runs with NextSeq550

  • 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

      2 x 75 50-60
      1 x 75 25-30

    Mid Output Flow Cell**

    2 x 150

    32-39

      2 x 75 16-19

             * Up to 400 M single reads, and up to 800 M paired-end reads
           ** Up to 130 M single reads, and up to 260 M paired-end reads

  • For details, contact: ngs (at) oulu.fi

Sequencing runs with Ion Torrent

  • 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:

    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

  • For details, contact: ngs (at) oulu.fi

Last updated: 3.12.2018