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.


Nodes


Node/Host UniversityNode 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; TAU: Tampere University; ÅAU: Åbo
Akademi University.



Contact details


Platform chair
Tapio Lönnberg, UTU, taplon@utu.fi

Platform vice-chair:
Minna Kaikkonen-Määttä, UEF, minna.kaikkonen@uef.fi


Services


Single-cell services provided by sc -omics platformUHUHUEFUTUUTU
Service categoryServiceSCAScProtGenSCGCSCOREMCy
SC transcriptomics (10X Chromium)3´gene expressionXXXX
5´and V(D)J gene expressionXXX
Fixed RNA profilingXXX
SC transcriptomics (BD Rhapsody)3´and V(D)J gene expressionX
SC epigenomics (10X Chromium)SC ATAC-seqXXXX
SC multiome (Chromium)ATAC + 3´gene expressionXXX
SC functional genomicsSC CRISPR screensXXX
SC iso-seq (Kinnex, MAS-seq)Long read sequencing of cDNA produced by 10XChromium 3´sequencing protocolX
SC genomics (Tapestri) SC DNA seqX
SC dispensing (cellenONE)Gentle, image based dispensing of single cells to any kind of plateX
Spatial gene expression (10X Visium)For FFPE samplesTrainingX
For fresh frozen samplesXTrainingX
Spatial gene expression (NanoString GeoMX)Training for customers to use by themselvesXX
Operator assisted service
Spatial gene expression
(subcellular level)
Training for customers to use by themselvesTBA
Operator assisted serviceTBA
Imaging mass cytometryOperator assisted serviceX
Imaging mass cytometryTraining for customers to use by themselvesX
Mass cytometryTraining for customers to use by themselvesX
Mass cytometryOperator assisted serviceX

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



Image
Image

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).