Tampere Genomics Facility is located in the Arvo building on the Kauppi Campus of the Tampere University. The facility offers instruments for a variety of genomics studies. After training by facility personnel, users can use the following instruments themselves:
Fragment Analyzer - nucleic acid analysis
TapeStation - nucleic acid analysis
MiSeq sequencing platform
Droplet Digital PCR
Chromium Controller - single cell molecular analysis
Covaris S220 ultrasonicator
Chemagic 360 robot - high throughput nucleic acid isolation
Janus G3 robot - automated liquid handling
The following service is performed by facility staff, who will run your ready-made reactions:
Sanger sequencing
More detailed information on the facility instruments can be found behind the Services tab.
Pricing
Please note that each instrument is billed differently. Prices for user groups from Tampere University are shown on each instrument's subpage. Other academic and non-academic users are asked to inquire specific pricing. Tampere Genomics Facility reserves the right to price adjustments.
The facility offers capillary electrophoresis instrument and materials for quantification and qualification of wide range of nucleic acids.
5200 Fragment Analyzer system is an automated instrument for the quantification and qualification of NGS libraries, gDNA and RNA. The facility provides the instrument and all reagents and materials required for performing an experiment. Customers prepare their samples and the instrument and perform the experiment(s) themselves.
We provide training for new users. Please contact persons responsible before using the instrument for the first time. For more information, please read the protocols:
Price per 11 samples (one row on a 96-well plate excluding ladder) is approximately 41 euros. Prices are adjusted based on possible changes in reagent and consumable costs.
Facility Technician:
Hanna Selin
hanna.selin(at)tuni.fi
Tel: +358 50 318 2119
Academic person in charge:
Heini Kallio
heini.kallio(at)tuni.fi
Tel: +358 50 318 5809
TapeStation
The Agilent 4150 TapeStation system is an automated electrophoresis platform that is meant for low-throughput analyses. It allows a quick and easy analysis of nucleic acids for up to 16 samples per run. Analysis takes 1 to 2 minutes per sample, or less than 20 minutes for 16 samples. The Agilent 4150 TapeStation system is the ideal solution for the quality control (QC) of RNA and DNA samples in next-generation sequencing (NGS), microarray and qPCR workflows.
The facility provides the instrument and all reagents for the following kits: D1000, HS D1000, D5000, RNA and genomic DNA. Researchers can perform their own runs independently after they have been trained by the facility technician Hanna Selin. In case you want to become a trained TapeStation user, ask a permission to use TapeStation through Agendo. Then book a time slot for your run and agree with Hanna Selin, hanna.selin(at)tuni.fi, about the details of the training.
Illumina MiSeq sequencing platform 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 data can be transferred from the MiSeq by BaseSpace or picked directly from the instrument.
Booking system
Booking system for the instrument: https://tuni.agendo.science (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:
For more information about the applications and prices, please contact Illumina’s Sr Territory Account Manager Sonja Klärck (E-mail: sklarck [at] illumina.comtitle="mailto:sklarck [at] illumina.com").
The kits and reagents for MiSeq are provided by users themselves. In addition, a small fee of approximately 46 euros per day is charged from users by facility.
NGS Service Managers:
Kati Rouhento
kati.rouhento(at)tuni.fi
Tel: +358 50 318 6866
Päivi Martikainen
paivi.martikainen(at)tuni.fi
Tel: +358 40 190 1260
Sanger sequencing
Sanger sequencing facility at Kauppi campus is situated in Arvo building 2nd floor, room E215, and it houses Applied Biosystems 3500xL Genetic Analyzer run by a core technician. ABI 3500xL is a 24-capillary instrument capable for running 2 x 96 samples (sequencing or fragment analysis) at a time.
The instrument is operated by the sequencing core staff who will run your ready-made reactions. Our service routinely delivers the results of pre-ordered runs in 24 hours of samples left from Monday to Thursday, provided that the samples with sample list are delivered to sequencing service by 14:30. Results of samples left on Friday afternoon by 14:30 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 Result Group to be used in the sample sheets. Sequencing results are collected based on the Result Group and a link to the results is sent to the customer by the core personnel. The link will be valid for max two weeks. 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™ v3.1 Chemistry (Sanger sequencing) starting with the manufacturers protocol. Please note that only 0.2 ml MicroAmp™ 8-Tube Strips and 0.2 ml MicroAmp™ Optical 96-Well Reaction Plates can be used in ABI 3500xL.
Sequencing is pre-ordered from sequencing(at)tuni.fi preferably two working days beforehand, or at latest on the previous working day by noon. Please inform us how many samples (x24) do you have and whether they are over or under 850 bp.
The customers make the sequencing samples ready for run themselves (cycling, cleaning, and suspension in HiDi Formamide).
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 customer and then sent in Excel 97-2003 Workbook form (.xls) to sequencing(at)tuni.fi. Instructions and links to sheets below.
Deliver samples either on 200 µl stripsin sets of 24 (n x 24, empty tubes filled with HiDi at least 12 µl /well) or on full200 µl sequencing plates (96 samples) to a provided rack inside a blue box in cold room E218.
Only MicroAmp™ plastics are allowed for sequencing and fragment analysis. Please note that any other strips or plates cannot be used with ABI 3500xL! Accepted plastics can be collected from the basic equipment cabinets on 2nd and 3rd floor corridors near the sequencing facilities.
Accepted strips are MicroAmp™ 8-Tube Strips, 0.2 ml
Accepted plate is MicroAmp™ Optical 96-Well Reaction Plate, 0.2 ml
You may use for example MicroAmp™ 8-Cap Strips to seal your strips or plates.
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.
If you are using strips mark the beginning sample number on one end of the strip (1, 9, 17, 25 etc.). Place your strips on the Sequencing service rack starting from A1. (Your 1st sample to position A1, your 9th sample to position A2, etc.)
If you are using plate you will be charged for the whole plate (4 x 24 samples). All wells have to be filled with HiDi (at least 12 µl /well). Make sure your sample number 1 is in well A1 on your plate, sample number 2 is in well B1 etc. Place the plate on the Sequencing service rack also starting from A1.
Deliver your samples and the sample list by 14:30. Samples are ran in first-come-first-serve basis provided that the pre-order to sequencing [at] tuni.fi (sequencing(at)tuni.fi )has been done. In case of backlog the samples and sample list arrived last will be sequenced on following day.
We will send a link to your sequencing results by e-mail when the results are ready. Results are transferred using Funet FileSender, and the link is valid for maximum of two weeks.
If you are running fragment analysis, please contact sequencing [at] tuni.fi (sequencing service)rel="noopener" target="_blank" for information.
On Excel, fill the Plate Name on cell A4 in the following way: DDMMYYYY_initials. You may also add an identifier (for example 03092018_NN_exon1). Maximum number of characters is 30.
Add Sample Names from cell B7 downwards and add the Results group (see table
to find the correct group name) from the cell E7 downwards. (Please note that the name of the Results group is case sensitive.) Add the Owner Name (for example your name).
Sample Name cannot be number only! It has to contain other character also (letters or for example underscore).
Disallowed characters are: space / * ” – + : ? ’ ,| ä ö å
In case your group doesn’t exist in Results group list please contact sequencing service.
Unless you have a full plate remove unnecessary information from columns C, D, and F. For example, if you’re running 24 samples, remove data from row 31 downwards by painting the cells C31-F102 and pressing delete button. Leave the column A (Well Positions) untouched.
When the sample sheet is ready, rename it with your Plate Name (DDMMYYY_initials) and send it in table form (.xls) to sequencing(at)tuni.fi.
Additional information
Short and long sequences as well as fragment analysis can be run in a same plate as long as there is 24 (x n) of each. Please ask additional information from sequencing [at] tuni.fi (sequencing service)rel="noopener" target="_blank" if you need to combine these different sample types in a same run.
The sequencing of long (>850 bp) products will take approximately 2 hours per injection, i.e. 1 x 24 samples. The fragment analysis and the sequencing of shorter products will take approximately 1 hour per one injection (1 x 24 samples).
With ABI 3500xL only MicroAmp™ plastics are accepted. They can be collected from the basic equipment cabinets on 2nd and 3rd floor corridors near the sequencing facilities. Links to manufacturer’s sites:
Price per 1 x 24 samples is approximately 33 euros. Prices are adjusted based on possible changes in reagent and consumable costs.
Sanger Sequencing Service email:
sequencing(at)tuni.fi
Sanger Sequencing Service Manager:
Kati Rouhento
kati.rouhento(at)tuni.fi
Tel: +358 50 318 6866
Sanger Sequencing Service Vice Manager:
Päivi Martikainen
paivi.martikainen(at)tuni.fi
Tel: +358 40 190 1260
Droplet Digital PCR
Droplet digital PCR (ddPCR) is a method for performing digital PCR that is based on water-oil emulsion droplet technology. A sample is fractionated into 20 000 droplets, and PCR amplification of the template molecules occurs in each individual droplet. ddPCR technology uses reagents and workflows similar to quantitative PCR. The massive sample partitioning is a key aspect of the ddPCR technique.
The facility provides the instruments and all reagents and materials required for droplet generation and droplet reading. Customers prepare their samples and perform the experiments themselves.
We provide training for new users. Please contact persons responsible before using the instrument for the first time. For more information, please read the protocol:
Chromium Controller - single cell molecular analysis
The Chromium Controller manufactured by 10xGenomics uses advanced microfluidics to perform single cell partitioning and barcoding in a matter of minutes. Powered by Next GEM technology, the Chromium Controller enables integrated analysis of single cells at massive scale. Chromium Single Cell products can capture molecular readouts of cell activity in multiple dimensions, including gene expression, cell surface proteins, immune clonotype, antigen specificity, and chromatin accessibility. The key to this technology is its ability to generate tens of thousands of single cell partitions, by encapsulating fed cell suspensions into single cell -containing oil droplets, each including an identifying barcode for downstream analysis. You can process between 1–8 samples in one run, loading up to 10,000 cells per sample.
Booking system
Researchers can use Chromium Controller after they have been trained by the facility personnel. Reservations are made using Agendo: https://tuni.agendo.science (Chromium Controller)
Select the correct products and respective manuals for your experimental needs from the 10xGenomics web site. It is advisable to invest some time on reading about this technology beforehand so that project’s needs can better meet product choice.
The usage of Chromium Controller is free of charge until otherwise informed. Chromium core facility provides certain plastics and general reagents needed in the experiments but researchers need to buy Chromium assay kits themselves.
Academic persons in charge:
Heini Kallio
heini.kallio(at)tuni.fi
Ismaïl Hermelo
ismail.hermelo(at)tuni.fi
Covaris S220 ultrasonicator
The Covaris S220 ultrasonicator is a versatile, high power system engineered for pre-analytical sample processing using Covaris’ patented Adaptive Focused Acoustics® (AFA®). It can be used for several applications such as DNA/RNA/chromatin shearing, DNA/RNA/total NA/protein extraction from FFPE, as well as tissue and cell lysis and extraction. A single tube can be processed at a time.
The facility offers Covaris S220 instrument that customers can use independently after they have been trained by facility personnel.
The shearing tubes needed for Covaris are provided by users themselves. In addition, a small fee of 10 euros per booking is charged from users by facility.
Academic person in charge
Heini Kallio
heini.kallio(at)tuni.fi
Tel: +358 50 318 5809
PerkinElmer Chemagic™ 360
Chemagic™ 360 is a magnetic bead-based nucleic acid isolation system suitable for human genetics (NGS, MLPA, genotyping and PCR), biobanking, HLA typing and virus and bacteria detection applications. A large amount of kits for the isolation of gDNA, cfDNA, totalRNA as well as viral and bacterial nucleic acids compatible with various specimens (whole blood, saliva, plasma, feces, tissues, FFPE samples etc.) are available.
The system is configurable with three kinds of Chemagic Rod Heads (12, 24 and 96) and it can process sample volumes from 10 µl to 10 ml. LIMS-compatible barcode reading, sample tracking and log files are obtainable for regulated workflow. Usually processing time is one hour but is depending on used protocol and modification needs.
The Tampere Genomics Facility provides the instrument and users can perform their own runs independently after they are familiar with the procedure. If you want to use Chemagic™ 360, please contact Nina Peltonen: nina.peltonen(at)tuni.fi. Later in June 2021 the instrument can be booked via Agendo.
Usage fee is 50 euros per day and 25 euros per 4 hours.
Facility Technician
Nina Peltonen
nina.peltonen(at)tuni.fi
PerkinElmer Janus G3 Varispan8 with gripper
Janus G3 automated liquid handling workstation is suitable for multiple pipetting and sample preparation procedures from ELISA to qPCR. Few ready-to-use protocols which can be modified depending on user’s needs and labware are available. Optionally, protocol can be programmed together with user according to user’s specific needs.
The system is equipped with 8-tip Varispan™ Arm with Versatips™, Gripper Arm, 500 µl syringes, barcode scanner, cooling/heating incubation station, ring magnet station, INHECO ThermoShake and vacuum filtration system. There is a possibility of automatically switching between fixed and disposable tips during the assay.
The Tampere Genomics Facility provides the instrument and users are encouraged to use workstation independently after they are familiar with the procedure. Potential Janus G3 users, please contact Nina Peltonen: nina.peltonen(at)tuni.fi. Later in June 2021 the instrument can be booked via Agendo.
Usage fee is 50 euros per day and 25 euros per 4 hours.
Tampereen yliopisto ja Tampereen ammattikorkeakoulu muodostavat monialaisen Tampereen korkeakouluyhteisön. Tutkimuksen ja opetuksen vahvuusalueita ovat tekniikka, terveys ja yhteiskunta.
Yliopiston puhelinvaihde: 0294 5211 Ammattikorkeakoulun puhelinvaihde: 0294 5222
