Single-Cell Omics | Biocenter

Single-cell omics platform develops and provides open-access single-cell and spatial transcriptomics services nationally and internationally. Sc omics collaborates very closely with the Biocenter Finland Genome-wide methods and Bioinformatics platforms.

Sc omics platform aims at bringing the latest single cell omics tools and technologies available for the research community. There are services available for single cell genomics (based on Missionbio Tapestri), single cell transcriptomics (Chromium by 10XGenomics), single cell epigenomics (Chromium by 10XGenomics) and single cell proteomics (Helios™ mass cytometry) to enable cutting-edge research in many areas of molecular biology and molecular medicine. In addition to single cell omics our platform has focused on providing services for spatial omics both on cellular level (Visium by 10XGenomics, GeoMX DSP by NanoString and Hyperion by Standard Biotools) and sub-cellular level (spring 2024).

Besides providing services sc omics platform is actively implementing new technologies, developing services, and participating in training of the users.

Contact details

Nodes

Services

Recent user publications

Nodes

Node/Host University	Node PI
Single-cell omics core facility (SCORE), UTU&ÅAU	Tapio Lönnberg, UTU, taplon@utu.fi
Single-Cell Analytics (SCA), UH	Jenni Lahtela, UH, jenni.lahtela@helsinki.fi
Single-cell Proteomics and Genomics (SCProtGen), UH	Martyn James, UH, martyn.james@helsinki.fi
Single Cell Genomics Core (SCGC), UEF	Minna Kaikkonen-Määttä, UEF minna.kaikkonen@uef.fi
Single cell proteomics (MCy), UTU&ÅAU	Pia Rantakari, UTU pia.rantakari@utu.fi

UEF: University of Eastern Finland; UH: University of Helsinki; UO: University of Oulu; UTU: University of Turku; ÅAU: Åbo Akademi University.

Contact details

Platform Chair

Tapio Lönnberg
taplon@utu.fi

Platform Vice Chair

Minna Kaikkonen-Määttä
minna.kaikkonen@uef.fi

Services

Single-cell services provided by sc -omics platform		UH	UH	UEF	UTU	UTU
Service category	Service	SCA	ScProtGen	SCGC	SCORE	MCy
SC transcriptomics (10X Chromium)	3´gene expression	X	X	X	X
	5´and V(D)J gene expression	X		X	X
	Fixed RNA profiling	X		X	X
SC transcriptomics (BD Rhapsody)	3´and V(D)J gene expression			X
SC epigenomics (10X Chromium)	SC ATAC-seq	X	X	X	X
SC multiome (Chromium)	ATAC + 3´gene expression	X		X	X
SC functional genomics	SC CRISPR screens	X		X	X
SC iso-seq (Kinnex, MAS-seq)	Long read sequencing of cDNA produced by 10XChromium 3´sequencing protocol		X
SC genomics (Tapestri)	SC DNA seq	X
SC dispensing (cellenONE)	Gentle, image based dispensing of single cells to any kind of plate	X
Spatial gene expression (10X Visium)	For FFPE samples			Training	X
	For fresh frozen samples	X		Training	X
Spatial gene expression (NanoString GeoMX)	Training for customers to use by themselves	X			X
	Operator assisted service
Spatial gene expression (subcellular level)	Training for customers to use by themselves			TBA
	Operator assisted service			TBA
Imaging mass cytometry	Operator assisted service					X
Imaging mass cytometry	Training for customers to use by themselves					X
Mass cytometry	Training for customers to use by themselves					X
Mass cytometry	Operator assisted service					X

Recent user publications

Pajanoja et. al.2023. Maintenance of pluripotency-like signature in the entire ectoderm leads to neural crest stem cell potential. Nat Commun 14, 5941.https://doi.org/10.1038/s41467-023-41384-6

Balboa et al., 2022. Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells. Nature Biotechnology, 40, 1042-1055.https://doi.org/10.1038/s41587-022-01219-z.

Huuhtanen et al. 2022. Single-cell characterization of leukemic and non-leukemic immune repertoires in CD8+ T-cell large granular lymphocytic leukemia.Nat Commun 13, 1981 (2022).https://doi.org/10.1038/s41467-022-29173-z

Alitalo et al, 2023. The angiopoietin receptor Tie2 is atheroprotective in arterial endothelium. Nat Cardiovasc Res. 2023 Mar 13;2(3):307-321. https://doi: 10.1038/s44161-023-00224-y.

Karaman et al. 2022, Interplay of vascular endothelial growth factor receptors in organ-specific vessel maintenance. J Exp Med (2022) 219 (3): e20210565.https://doi.org/10.1084/jem.20210565

Schematic figure caption of the MAS-seq protocol (left) and size distribution of a MAS-seq data produced from a 10x single cell cDNA library with PacBio Sequel 2 machine (right).