Genomic and transcriptomic sequencing

• Illumina Sequencing Coverage Calculator
• Illumina NGS Methods Guide

Extract your RNA with preferred kit (e.g. Qiagens RNeasy Mini Kit (Catalog no. 74104) with Optional On-Column DNase Digestion with the RNase-Free DNase Set (cat. no. 79254)). Please, be sure that your RNA samples are free from DNA, as this will result in an underestimation of the amount of RNA used.

From extracted RNA, three aliquots should be separated before freezing to avoid extra freezing-thawing cycles. These aliquots need to present the sample-aliquots to be sequenced, so no dilutions, or additional freezings for these.

• First aliquot (preferably 8 µl/sample) is for measuring precise concentration of samples with Qubit-assay.
• The second aliquot (2 µl/sample) is for Bioanalyzer-assay for determining the RNA Integrity Number (RIN)-values.
• The third aliquot (15-20 ul) is used for library preparation.

Please contact to ngs (at) oulu.fi for any questions, or if you have only limited amount of RNA.

The purity and approximate concentration should be measured for all samples (e.g. NanoDrop). The recommended thresholds are:

• 260/280 value 1.7-2, preferably 1.8
• 260/230 value > 1.5, preferably > 1,8

Please send this information (purity/concentration) to ngs (at) oulu.fi, to receive instructions how to proceed.

• 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
• Contact: katri.pylkas (at) oulu.fi, ngs (at) oulu.fi

• 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

• DNA samples are sequenced up to 12 sample batches with Illumina NextSeq550 instrument
• Customer delivers purified DNA samples.
• 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

• Libraries can be prepared for various gene panels utilizing Nextera rapid capture chemistry
• Customer delivers purified DNA samples.
• 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

• 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

• 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

• 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

Ion Torrent PGM support by Thermo-Fisher Scientific will end officially 31.12.2023. Limited number sequencing runs with 316 chip will still be available 2024 in our lab. Please inquire more from marko.suokas(at)oulu.fi, if you still have samples, you wish to sequence with Ion Torrent.

We are also currently transferring our amplicon sample preparation services to support Illumina sequencing platforms (mainly aimed towards Illumina MiSeq instrument). Services will be available 2024 and sequencing outsourced.