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cer cell signaling research description ongoing projects lab members outside the lab publications open positions kauko lab cancer proteomics research description lab members turku proteomics facility publications ivaska lab cell adhesion and cancer research description ivaska lab members ivaska publications jacquemet lab cell migration research description lab members elo lab computational biomedicine research description lab members eriksson lab cytoskeletal and survival signaling research description ongoing projects eriksson lab members eriksson publications paatero lab i disease models lab members selected publications alanko lab immune cell navigation research description immune cell navigation lab members publications coffey lab kinase function in brain research description kinase function lab members publications and preprints papageorgiou lab protein structure and fucntion research description ongoing projects lab members publications rantakari lab macrophage ontogeny and function research description lab members publications lahesmaa lab molecular systems immunology research description lab members ongoing projects publications courtney lab neuronal signalling pathways research description ongoing projects lab members publications news dickens lab neurometabolomics research description lab members publications metabolomics core turku centre for chemical and molecular analytics ccma lönnberg lab single cell immunogenomics research description lab members publications orešič lab systems medicine research description ongoing projects lab members selected publications affiliates figueiredo lab melanoma immune oncology gramolelli lab viral oncogenesis kaslin lab i cellular plasticity in brain and spinal cord knip lab pediatric diabetes mattila lab lymphocyte activation lab najumudeen lab stem cell metabolism in health and cancer pentikäinen lab up lab peuhu lab breast development and cancer sahlgren lab cell fate sistonen lab heat shock response goes beyond cell stress zhang lab functional materials for medicine ventelä lab head and neck cancer research updates news events blog publications vacancy contacts personnel openiris log in login search for finnish functional genomics centre finnish functional genomics centre about us services pricing instruments ngs project request submit your publication education and training contact publications services genome analysis transciptome analysis epigenome analysis microbiome analysis sequencing of ready made ngs libraries sample requirements ngs quantitative real time pcr sample delivery ngs 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 send an email to ffgc at 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 twist exome 2 0 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 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 send an email to ffgc at 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 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 send an email to ffgc at bioscience fi and we will contact you as soon as possible sample requirements general sample requirements can be found from the tab sample delivery 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 unavailable at the moment 12 25 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 send an email to ffgc at 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 unavailable at the moment 12 25 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 novaseqx and miseq i100 plus sequencing instruments for service use illumina novaseq x has three different flow cells and different read lengths can be combined into same run we will combine different projects to same runs so individual lanes can be purchased more information about novaseqx sequencing specifications can be found from here illumina miseq i100 plus can be used for sequencing of smaller projects with up to 2x500bp read lengths more information about miseq sequencing specifications can be found from here for further information please send an email to ffgc at 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 i100 plus 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 at bioscience fi for detailed instructions novaseqx sequencing minimum concentration of 4 nm for ready library pool or 1 8 separate pools depending on the used flow cell and number of used lanes 15 ul for 1 5b and 10b for one lane 25 ul for 25b for one lane the concentration and volume depend on the flow cell and application please contact ffgc at 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 f luid x 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 c oncentration 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 a nd 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 si milar 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 a lternative 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 qu ality 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 ba lance 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 samples can be delivered to ffgc office in biocity 5 th floor on mondays 9 11 or on thursdays 13 15 please agree beforehand more precise delivery time for samples samples should be sent to us well packed with enough dry ice using the courier service of your ...