Genome Analysis

Our genome analysis services include full range of options from targeted analysis of known variants to genome sequencing. Our next-generation sequencing based solutions for Genome analysis include:

• Whole Genome Sequencing (Illumina DNA PCR-free and Illumina DNA prep)
• Exome Sequencing (Twist Comprehensive exome)

The service includes QC of the DNA, library preparation, next-generation sequencing and QC analysis of the raw data. For further information please fill in our NGS Project Request Form or send an email to ffgc@bioscience.fi, and we will contact you as soon as possible.

Sample Requirements

General sample requirements can be found from the tab "Sample delivery". Illumina DNA PCR-free

• Product page
• 700 ng genomic DNA for standard protocol
• Suitable for larger genomes
• Accredited method for human samples
• Recommended concentration > 15 ng/ul, minimum volume 10 ul
• >300 ng recommended input
• Library preparation can be started with less material but please contact us in this case

Illumina DNA prep

• Product page
• 300-500 ng genomic DNA for larger genomes
• 10-100 ng genomic DNA for small genomes (bacteria etc.)
• Recommended concentration >10 ng/ul, minimum volume 10 ul

Twist Comprehensive exome

• Product page
• Human samples only
• Accredited method
• 300-500 ng genomic DNA
• Recommended concentration 20-50 ng/ul, minimum volume 10 ul
• Samples processed in sets of 8

Transcriptome Analysis

Transcriptome analysis enables characterisation of coding and non-coding RNAs present in cells or tissues as well as comparison of gene expression or RNA isoform levels between different conditions. With deep sequencing it is also possible to characterise de novo transcriptomes and coding variants. According to your needs, we offer either full or partial service for transcriptome analysis by using next-generation sequencing based solutions:

• total RNA (Illumina stranded total RNA prep)
• polyA+ RNA, mRNA (Illumina stranded mRNA prep)
• small RNA, miRNA (Qiaseq miRNA library kit)

The service includes QC analysis of nucleic acids, library preparation, next-generation sequencing and QC analysis of the raw data. The cost of the service depends e.g. on application, number of samples and required sequencing depth. For further information please fill in our NGS Project Request Form or send an email to ffgc@bioscience.fi, and we will contact you as soon as possible.

Sample Requirements

General sample requirements can be found from the tab "Sample delivery". Illumina stranded total RNA prep with Ribo-zero Plus

• Product page
• 500 ng of total RNA
• Library can be started from 10-100 ng of total RNA
• Recommended concentration >10 ng/ul, minimum volume 10 ul
• Protocol includes removal of ribosomal RNA

Illumina stranded mRNA prep

• Product page
• 500 ng of total RNA
• Library can be started from 25-100 ng of total RNA
• Recommended concentration > 10 ng/ul, minimum volume 10 ul

Qiaseq miRNA library kit

• Product page
• 300 ng of total RNA or 30 ng of small RNA
• Library can be started from 10-100 ng of total RNA or 1-10 ng of small RNA
• Recommended concentration >10 ng/ ul, minimum volume 10 ul

Epigenome Analysis

Genome function is directed by epigenetic regulation through chemical modifications of DNA, DNA bound proteins and by noncoding RNAs. Epigenetic regulation is crucial for the proper development and function of cells and tissues. Epigenetic modifications regulate organization and packaking of chromatin and control activity and accessibility of important functional elements of the genome, such as promoters and enhancers. Epigenetic regulation is sensitive to environmental and life style factors, which can cause both temporary and long-term changes in the genome. These changes can further influence development, traits and health of an individual. Our next-generation sequencing based solutions for epigenome analysis include:

• Reduced Representation Bisulfite Sequencing (RRBS) (Tecan Ovation RRBS Methyl-Seq) (unavailable due to discontinuation of the kit by Manufacturer from 01/25, new kit will be tested)
• Whole Genome Bisulphite Sequencing (WGBS) (temporarily unavailable)
• EMseq method in testing (12/24)

The service includes QC analysis of the DNA, library preparation, next-generation sequencing and raw data QC. For further information please fill in our NGS Project Request Form or send an email to ffgc(a)bioscience.fi, and we will contact you as soon as possible.

Sample Requirements

General sample requirements can be found from the tab "Sample delivery". Tecan Ovation RRBS Methyl-Seq

• Product page
• 500 ng genomic DNA
• Recommended concentration 50 ng/ul, minimum volume of 10 ul

Microbiome Analysis

Our Microbiome analysis service enables identification of bacterial strains or fungal rRNAs present in a sample of interest, such as stool or environmental specimens. Our next-generation sequencing (NGS) based solutions for Microbiome analysis include:

• Targeted Amplicon Sequencing (e.g. 16S/18S/ITS) (limited availability)
• Metagenomic Shotgun Sequencing (Illumina DNA prep)

The service includes nucleic acid QC, sample preparation, next-generation sequencing and raw data QC. For further information please fill in our NGS Project Request Form or send an email to ffgc(a)bioscience.fi, and we will contact you as soon as possible.

Sample Requirements

General sample requirements can be found from the tab "Sample delivery". Targeted Amplicon sequencing (16S/18S)

• Used protocol
• Primers in the above mentioned protocol are used or other primers that customer has tested to be functional in the protocol
• DNA concentration 5 ng/ul, volume 10 ul
• No QC is done for the samples prior to analysis

Illumina DNA prep

• Product page
• 300-500 ng genomic DNA for larger genomes
• 10-100 ng genomic DNA for small genomes (bacteria etc.)
• Recommended concentration >10 ng/ul, minimum volume 10 ul

Sequencing of ready-made NGS libraries

FFGC offers Next-Generation Sequencing (NGS) for various types of ready-made NGS-libraries prepared by our users. We have Illumina Novaseq6000 and MiSeq sequencing instruments for service use. The MiSeq instrument is also available for open-access use. Illumina Novaseq 6000 has four different flow cells and several different read lengths available. More information about Novaseq6000 sequencing specifications can be found from here. Illumina MiSeq can be used for sequencing of smaller projects with up to 2x300bp read lengths. More information about MiSeq sequencing specifications can be found from here. For further information please send an email to ffgc(a)bioscience.fi, and we will contact you as soon as possible.

Sample Requirements

General sample requirements can be found from the tab "Sample delivery".

• Provide your libraries as a ready library pool
• QC of library pool is included in the price of sequencing
• PhiX can be added to sequencing according to library type. PhiX is included in the price of sequencing.

MiSeq sequencing as a service

• Minimum  concentration of 4 nM for ready library pool
• Minimum volume of 20 ul
• The concentration and volume depend on the flow cell and application, please contact ffgc(a)bioscience.fi for detailed instructions

Novaseq6000 sequencing 

• Minimum concentration of 4 nM for ready library pool or 1-4 separate pools depending on the used flow cell
• 40-350 ul volume
• The concentration and volume depend on the flow cell and application, please contact ffgc(a)bioscience.fi for detailed instructions.

General sample requirements

• If the sample number is more than 10, use either 8-tube strips or 96-well PCR plates ( or FluidX tubes). Do not leave empty wells or columns in the middle of the plate. Full reaction cost is invoiced for empty wells.
• All samples must be normalised to same concentration. Additional fee will be applied, if samples are delivered in wrong/varying concentration.
• When diluting samples, concentration of the sample should be based on fluorometric measurement method.
• Place the samples in defined well order column wise (A1, B1, C1, D1 etc) to the PCR plate and include max 94
  samples in 96-well plate.
• Plates must be sealed carefully with a PCR plate seal.
• FFGC personnel will contact you about the results of the QC analysis. If samples with low quality are detected, you can replace them with new ones if possible.

Genomic DNA samples

• Genomic DNA should be intact and pure, and free of RNA or small nucleic acid fragments, such
  as nucleotides, or other contaminants
• The ratio of absorbance 260 nm/280 nm is of 1.8 (+/-0.2)
• DNA sample should contain < 1 mM EDTA and be free of phenol, ethanol and other organic
  contaminants.
• DNA that has RNA contamination will result in underestimation of the amount of DNA used. To
  prevent this, RNase step is recommended.
• If there is not enough starting material or enough good quality material available, alternative workflows exist and can be discussed separately. However, FFGC does not guarantee results for samples with low DNA quality.

Total RNA samples

• Total RNA should be intact and pure.
• The Agilent Bioanalyzer RIN or Fragment Analyzer RQN value should be > 7.0, when
  applicable.
• The ratio of absorbance 260 nm/280 nm is 2.0 (+/-0.2).
• All samples should have similar quality.
• RNA that has DNA contamination will result in underestimation of the amount of RNA used. To prevent this, DNase step is recommended, but not required, to be included with the RNA isolation method.
• If good quality material is not available, alternative workflows exist, and can be discussed separately.
  When using low quality total RNA samples (RIN value < 7.0) for library preparation, all samples should
  be similar and equally degraded. FFGC does not guarantee results for samples with low RNA quality.

Ready-made libraries

• Library fragments should have compatible size distribution with selected read length and
  sequencing instrument according to the library preparation protocol recommendations.
• When several libraries are pooled in one run, it is important to maintain color balance for each base of the index read for optimal de-multiplexing. FFGC personnel can assist in the selection of color-balanced indexes before library preparation.
• Please, note that FFGC does not take any responsibility of the quality of sequencing results for ready-made libraries. 

Plate Running Service

The Plate running service is intended only for user-prepared plates. We are running plates as a service at the beginning of each week, Monday-Wednesday. The rest of the week is reserved for users who run plates themselves. If you are interested to operate QuantStudio independently, please contact taqman (at) utu.fi and ask for training (this option is only possible for Turku Bioscience groups). We currently operate QuantStudio™ 12K Flex Real-Time PCR System (Thermo Fisher Scientific). When you bring a plate to us, below is a list of details you should consider. You have the right plate format. We can run:

• 96-well plates (4titude, 4ti-0912 or equivalent, semi-skirted, barcoded plate).
• 384-well plates (4titude,4ti-0384 or equivalent, skirted, barcoded plate).

Both plate types and plate seals are available through our plastic ware storage. Please note that all plates coming to the plate running service need to be barcoded. For those users who do not have access to our common storage: please send your plasticware order by emailing taqman (at) utu.fi. We will deliver your order to the Turku Bioscience parcel drop zone. 96 and 384 well plates are sold in packages of 10 and seals are sold in packages of 100. Prepare your plate, put it in a plastic (minigrip) bag, identify the bag with your name and bring it to the cold room “Kyösti” into a box “qPCR Plate Running Service” in Biocity, A-stairs, 5th floor (BTK). Make the run file (eds.file) for your plate with QuantStudio 12K analysis software. Please select the correct block type, either 384-Well or Fast 96-Well (0.1ml). Thermo Fisher provides software options for data analysis:

• Thermo Fisher Cloud is the recommended way to view and analyze your run data. You can access the cloud here.
• QuantStudio 12 K Flex software is used with QuantStudio instrument for creating and analyzing plate run files. To get your copy of the QuantStudio software, please contact us at taqman (at) utu.fi (only for our plate running service users).

Send the EDS file as an e-mail attachment to taqman (at) utu.fi. If your 96 well plates and run files are submitted in the plate running service before 1 pm, they will be placed on the running queue of the same day and you will get the results during the next workday. Do not bring plates any more on Wednesdays after 1 pm. The 384 plates you can bring only on Mondays or Tuesdays and we will run them during the same week, when there is suitable time to change the block. If you would like to get the plate back, please mention it in the email.  

Sample delivery