BioMediTech Research Infrastructure

NGS & Sanger Sequencing

The facility offers the use of Illumina MiSeq sequencer for a wide range of next-generation sequencing. In addition, the facility offers Sanger sequencing for researchers’ ready-made sequencing reactions.

Introduction

Sanger sequencing

Sequencing facility at Kauppi campus is situated in Arvo building 2nd floor, room E215, and it houses two ABI3130xl Genetic Analyzers (Mauno, Maire) run by a core technician. During daytime Mauno and Maire are operated by the sequencing core staff who will run your ready-made reactions. Our service routinely delivers the results in 24 hours of samples left from Monday to Thursday. Results of samples left on Friday afternoon will be ready next Monday morning. In case of any delays we will contact you by email.

At the first time our customer (research group) gets a password protected domain where the results are saved for one month. Be sure to collect your data during that time.

The service is run-only with auto-analysis of raw data from ready-made samples. We recommend usage of ABI BigDye Chemistry (Sanger sequencing) starting with the manufacturers protocol.

We are open-minded and ready to develop our service according to comments from our customers.

NGS

Illumina MiSeq sequencer for targeted and small genome sequencing is located in Arvo building 2ndfloor, room E215. The system enables a broad range of applications, from targeted gene sequencing to metagenomics, small genome sequencing, targeted gene expression analysis, and more. Customers prepare the sample libraries and order all the reagents for the instrument by themselves. The instrument is run by facility technician, or by customer after user training provided by the core personnel. The data can be transferred from the MiSeq by BaseSpace or picked directly from the instrument.

Booking system for the instrument: https://next.cirklo.org/biomeditech / (MiSeq). All information about the run is also written down to the logfile next to the instrument.

Read more about the instrument from the manufacturers web site:
http://www.illumina.com/systems/miseq.html

For more information about the applications and prices, please contact Illumina’s Finnish Territory Account Manager Reija Laitinen (Cell: +358 40 521 2847, E-mail: rlaitinen@illumina.com).

Instructions

Sanger sequencing

The customer makes the sequencing samples ready for run themselves (cycling, cleaning, and suspension in HiDi Formamide, denaturing). You can use our convenient Freezer Program to purchase BigDye Terminators and HiDi.

Fill the sign-up list on the freezer and the products will be charged with your sequencing bill. The Buffer for BDT is available in cold room E218 in aliquots.

Sequencer plates or strips with purified sample in Hi-Di formamide are taken to the cold room
(instructions below). Sample sheets are modified by the researcher and then sent it in text form (tab) to sequencing(at)uta.fi.

  • Deliver samples either on 200 µl sequencing plates or strips in sets of 16 (n x 16, empty tubes filled with HiDi at least 12 µl /well) to a rack inside a blue box in cold room E218.
  • Fill in information about your samples to form found on a table outside the cold room. Please, remember also to add your phone number. Each row of the form has a running number.
  • Write this number clearly on a post-it slip found on the shelf and attach the slip to your sample rack.
  • Make clear markings which sample is sample number 1 on your plate. If you are using strips mark the beginning sample number on one end of the strip (1, 9, 17, 25 etc.).

We will send an e-mail when the results are in your own password protected domain.

Modifying sample sheet

  1. Choose the right sample sheet (excel):
    Sequence > 600 bp: Sequencing sheet 1 (50 cm)
    Sequence < 600 bp: Sequencing sheet 2 (36 cm)
  2. On Excel, change the container name on cell A2 in the following order: datemonthyear_identifier for example 03032012_exon1_Name. Maximum number of characters is 30.
  3. Add sample names from cell B6 downwards and add the results group from the cell E6 downwards. Add the owner (for example your group) and operator (for example your name).
    Disallowed characters for sample names and container name are: space / ( ) * ” – + : . ? ’ ,| ä ö å
  4. Remove unnecessary information from the table. For example, if you’re running 16 samples, remove all data from row 22 (well A03) downwards by painting the area and pressing delete button.
  5. When the sample sheet is ready, send it in text form (tab) to sequencing(at)uta.fi.

Text form:

Sequence > 600 bp: Sequencing sheet 1 (50 cm)
Sequence < 600 bp: Sequencing sheet 2 (36 cm)

Prices

Sanger sequencing

Price per each Sequencing run derives from actual operating costs (chemicals, consumables, instrument service contract and staff salary) divided by number of runs in the facility. Please inquire!

NGS

The kits and reagents for MiSeq are provided by users themselves. The costs for Illumina Product Care Service contract will be divided among the users according to the use.

Contacts

Sanger Sequencing Service email:

sequencing(at)uta.fi

Sanger Sequencing Service Manager:

Laboratory Technician
Kati Rouhento
kati.rouhento(at)uta.fi
Tel: +358 50 318 6866

Sanger Sequencing Service Vice Manager:

Hanna Selin
hanna.selin(at)uta.fi
Tel: +358 40 190 1260

NGS Service Manager:

Laboratory Technician
Kati Rouhento
kati.rouhento(at)uta.fi
Tel: +358 50 318 6866

Intranet

Intranet (password required)

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