The Genome-wide methods platform consists of seven nodes located at Helsinki, Turku, Tampere and Oulu. The network provides state-of-the-art genomics and transcriptomics services using high throughput genetic methods. The service portfolio includes a broad range of sequencing services including whole genome, whole exome, targeted panel, cell free DNA, transcriptome, metagenome and methylation sequencing as well as Sanger sequencing and genotyping. We are constantly also setting up new applications and welcome collaborative development projects supporting molecular biology and biomedical research. Our core facilities are coordinated by professional personnel and experts in the field and our services are based on the focus areas and expertise of the units within the platform. The platform participates actively in teaching and training, bringing the latest knowledge in genomics research and state-of-the-art technologies to the research community.


Contact details


Platform Chair: Kati Donner
kati.donner@helsinki.fi

Nodes


Node/Host UniversityNode PI
FIMM Genomics, UH
Kati Donner, UH
kati.donner@helsinki.fi
DNA Sequencing and Genomics
Laboratory (BIDGEN), UH
Petri Auvinen, UH
petri.auvinen@helsinki.fi
Biomedicum Functional Genomics
Unit (FuGU), UH
Outi Monni, UH
outi.monni@helsinki.fi
Genome Biology Unit (GBU), UH
Saara Ollila, UH
saara.ollila@helsinki.fi
BMT Cancer Genomics, TAU
Heini Kallio, TAU
heini.kallio@tuni.fi
Finnish Functional Genomics
Centre (FFGC), UTU
Minna Kyläniemi & Riikka Lund, UTU
minna.kylaniemi@utu.fi
riikka.lund@utu.fi*
BCO Sequencing Center, UO
Katri Pylkäs, UO
katri.pylkas@oulu.fi

UEF: University of Eastern Finland; UH: University of Helsinki; UO: University
of Oulu; UTU: University of Turku; TAU: Tampere University; ÅAU: Åbo
Akademi University. *Riikka Lund on partial leave of absence 2024



Services


FIMM Genomics


Whole genome, exome and targeted sequencing, transcriptomics, metagenomics and CRISPR screening, cfDNA and Sanger sequencing, fragment analysis, long read sequencing, TaqMan and array genotyping, methylation profiling with microarray and enzymatic methyl sequencing, cell line authentication, primary data analysis e.g. RNA-seq and miRNA data analysis, CNV analysis and variant filtering and annotation

DNA Sequencing and Genomics Laboratory


Sequencing of genomes and RNA samples from all kinds of origins using short read and long read approaches. Also Sanger sequencing of PCR fragments and plasmids preparations. Bioinformatics analysis for genomes when resources allow it.

Biomedicum Functional Genomics Unit


Sequencing (NGS) of exomes, genomes, transcriptomes (coding and non-coding) and targeted areas of the genome from various organisms. Bioinformatics services for analysis of the NGS data. Targeted gene and protein expression assays by NanoString and Olink systems.

Genome Biology Unit


Delivery of constructs from genome-wide collection of cDNA, shRNA and gRNA libraries, Gateway cloning and mutagenesis, gRNA and double gRNA design and cloning, pooled library construction and amplification, digitalization of microscopy slides.

BMT Cancer Genomics


Sanger sequencing, amplicon sequencing, droplet Digital PCR, single cell omics, spatial omics, automated DNA/RNA extraction, automated liquid handling, quantification and qualification of nucleic acids

Finnish Functional Genomics Centre


Human exome sequencing, whole genome sequencing, RRBS analysis, transcriptomics, metagenomics, bacterial 16S rRNA sequencing, sequencing of ready libraries

BCO Sequencing Center


Human exome sequencing, transcriptomics, metabarcode, bacterial 16S rRNA, and fungal ITS region sequencing, sequencing of customer prepared libraries, capillary sequencing, automatic DNA/RNA extraction, automated electrophoresis, optical genome mapping

Recent user publications


FIMM


Nuotio, M-L., Tähtisalo, H. S., Lahtinen, A., Donner, K., Fyhrquist, F., Perola, M., Kontula, K. K. & Hiltunen, T. P. Pharmacoepigenetics of hypertension: genome-wide methylation analysis of responsiveness to four classes of antihypertensive drugs using a double-blind crossover study design. 2022 Nov;17(11):1432−1445. 10.1080/15592294.2022.2038418. Methylation analysis and participation in the data analysis.

BIDGEN


Aho, VT., Crawford Houser, M., Pereira, PAB., Chang, J., Rudi, K., Paulin, L., Hertzberg, V., Auvinen, P., Scheperjans, F. & Tansey, MG. 2021. Relationships of gut microbiota, short-chain fatty acids, inflammation, and the gut barrier in Parkinson's disease. Molecular Neurodegeneration 16:6.PMID:33557896 doi: 10.1186/s13024−021−00427−6. Sequencing and data analysis was performed in BIDGEN.

FuGU


Ronkainen A, Khan I, Krzyzewska-Dudek E, Hiippala K, Freitag TL, Satokari R (2023) In vitro adhesion, pilus expression, and in vivo amelioration of antibiotic-induced microbiota disturbance by Bifidobacterium spp. strains from fecal donors, Gut Microbes, 15:1, DOI: 10.1080/19490976.2023.2229944. FuGU RNA-seq library preparation and NGS

GBU


Conway JRW, Dinç DD, Follain G, Paavolainen O, Kaivola J, Boström P, Hartiala P, Peuhu E, Ivaska J. IGFBP2 secretion by mammary adipocytes limits breast cancer invasion. Sci Adv. 2023. DOI: 10.1126/sciadv.adg1840. GBU provided cDNA clones.

BMT


Saralahti AK, Harjula SE, Rantapero T, Uusi-Mäkelä MIE, Kaasinen M, Junno M, Piippo H, Nykter M, Lohi O, Rounioja S, Parikka M, Rämet M. Characterization of the innate immune response to Streptococcus pneumoniae infection in zebrafish. PLoS Genet. 2023 Jan 9;19(1):e1010586. DOI: 10.1371/journal.pgen.1010586. BMT provided Sanger sequencing and Fragment Analyzer service.

FFGC


Suomi T, Kalim UU, Rasool O, Laiho A, Kallionpää H, Vähä-Mäkilä M, Nurmio M, Mykkänen J, Härkönen T, Hyöty H, Ilonen J, Veijola R, Toppari J, Knip M, Elo LL, Lahesmaa R. Type 1 Diabetes in Children With Genetic Risk May Be Predicted Very Early With a Blood miRNA. Diabetes Care. 2022 Apr 1;45(4):e77-e79. FFGC small RNAseq library preparation and NGS.

BCO


Kaisanlahti A , Turunen J , Byts N, Samoylenko A, Bart G, Virtanen N, Tejesvi MV, Zhyvolozhnyi A , Sarfraz S , Kumpula S, Hekkala J, Salmi S , Will O, Korvala J, Paalanne N, Erawijantari PP, Suokas M, Peñate Medina T , Vainio S, Peñate Medina O, Lahti L, Tapiainen T, Reunanen J. Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles. Microbiome. 2023;11(1):249. doi: 10.1186/s40168−023−01694−9. BCO NGS (16S rRNA) and data analysis


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NovaSeq6000 flow cells and the sequencer


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Available instrumentation


FIMM


MiSeq, NovaSeq 6000, iScan (Illumina), PromethION 2 Solo, MinION (ONT), ABI3730xl DNA Analyzer (Thermo)

BIDGEN


Miseq, Nextseq 500, Iseq, Novaseq 6000 (together with FIMM) (Illumina), Sequel II (PacBio from 2024 PacBio Revio), AVITI (Element Biosciences), PromethION 2 Solo (Oxford Nanopore), ABI Sanger sequencer ABI3500xL (Thermo), qPCR and ddPCR, Fragment analyser (Agilent), Bioanalyzer (Agilent) , Ionic (Purigen)

FuGU


MiSeq FGx, NextSeq500, TapeStation 4200, VictorNivo, NanoString nCounter FLEX, Fluidigm HD Biomark

GBU


ORFeome cDNA library, TRC1 shRNA library, Sanger gRNA library, Pannoramic 250 FLASH III scanner (3D Histech).

BMT


Fragment Analyzer, TapeStation, Illumina MiSeq, ABI 3500xL Genetic Analyzer, Bio-Rad ddPCR QX200 system, Covaris S220, PerkinElmer Chemagic 360, PerkinElmer Janus G3, GeoMx DSP, Visium CytAssist, Chromium iX

FFGC


Novaseq 6000, MiSeq (Illumina), Fragment Analyzer, Bioanalyzer, Quantstudio 12K Flex, Pyromark Q24 (Qiagen)

BCO


Illumina NextSeq550, Ion Torrent PG, ABI 3500xL Genetic Analyzer, Bionano Genomics Saphyr, QIASymphony, QIAqility, BioRad CFX96 Touch Real-Time PCR, Agilent 2100 Bioanalyzer