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Eukaryotic Single Cell Genomics (ESCG)

National facility

Single-cell analysis and single-cell RNA-sequencing technologies are rapidly advancing and have proven to give new insights into cell type discovery and in the characterization of heterogeneity in tumors as well as in normal tissue.

The Eukaryotic Single Cell Genomics (ESCG) facility aims at providing high-throughput single cell transcriptomics services to the Swedish and the international scientific community. We offer streamlined single-cell RNA sequencing at full-service. The user provide us with single cells, we process the samples, sequence and deliver annotated gene expression data.

  • Study heterogeneity within putatively homogeneous cell populations
  • Unbiased discovery of cell types in complex tissues
  • Characterizing the cellular and genetic composition of tumors



  • User Consultation and project design
  • Sample preparation support and QC
  • Single cell RNA-sequencing
  • Single nucleus RNA-sequencing
  • Single cell ATAC-sequencing
  • Single cell immune profiling
  • Sample multiplexing
  • Initial bioinformatics and QC analysis. We refer to NBIS for project specific bioinformatic analysis.


Single-Cell transcriptomics

  • 384-well plate based, smart-seq3
    • full-length, sensitive, quantitative, isoform reconstruction
  • Droplet-based, 3' gene expression, 5' gene expression
    • 10x Genomics
  • Microwell-based, full-length analysis
    • 5184-well plate, ICELL8 cx/TAKARA

Single-cell epigenomics 

  • Single Cell ATAC-sequencing
    • 10x Genomics

Single-cell immune profiling 

  • V(D)J profiling of T- and B-cells
    • 10x Genomics

Multi-omics single-cell profiling

  • Transcriptomics + protein
    • 10X Genomics + CITE-seq antibodies from Biolegend

Single-cell sample multiplexing

  • Cell hashing
    • 10x Genomics + hashing antibodies from Biolegend

Single-cell transcriptomics based CRISPR screens

  • Together with the High-throughput Genome Engineering facility, SciLifeLab
    • 10x Genomics


  • ECLIPSE Ti-E inverted microscope system, Nikon
  • Liquid handling robotic system, 96 & 384 head, TECAN EVO
  • NanoDrop low volume liquid dispenser, GC Biotech
  • SmartChip Multisample Nanodispenser (9600 wells), TAKARA
  • SMARTer ICELL8 cx single cell system (5184 wells), TAKARA
  • Chromium controller, 10X Genomics
  • Bioanalyzer, Agilent
  • Fragment Analyzer, Agilent
  • Cell culture room
  • Automatic Cell counter


A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart.

Asp M, Giacomello S, Larsson L, Wu C, Fürth D, Qian X, Wärdell E, Custodio J, Reimegård J, Salmén F, Österholm C, Ståhl PL, Sundström E, Åkesson E, Bergmann O, Bienko M, Månsson-Broberg A, Nilsson M, Sylvén C, Lundeberg J

Cell. 2019 Dec 12;179(7):1647-1660.e19. doi: 10.1016/j.cell.2019.11.025


A cell fitness selection model for neuronal survival during development

Wang Y, Wu H, Fontanet P, Codeluppi S, Akkuratova N, Petitpré C, Xue-Franzén Y, Niederreither K, Sharma A, Da Silva F, Comai G, Agirman G, Palumberi D, Linnarsson S, Adameyko I, Moqrich A, Schedl A, La Manno G, Hadjab S, Lallemend F

Nat Commun. 2019 Sep 12;10(1):4137. doi: 10.1038/s41467-019-12119-3.


Spatiotemporal structure of cell fate decisions in murine neural crest

Soldatov R, Kaucka M, Kastriti ME, Petersen J, Chontorotzea T, Englmaier L, Akkuratova N, Yang Y, Häring M, Dyachuk V, Bock C, Farlik M, Piacentino ML, Boismoreau F, Hilscher MM, Yokota C, Qian X, Nilsson M, Bronner ME, Croci L, Hsiao WY, Guertin DA, Brunet JF, Consalez GG, Ernfors P, Fried K, Kharchenko PV, Adameyko I

Science. 2019 Jun 7;364(6444). pii: eaas9536. doi: 10.1126/science.aas9536.


A molecular atlas of cell types and zonation in the brain vasculature.

Vanlandewijck M, He L, Mäe MA, Andrae J, Ando K, Del Gaudio F, Nahar K, Lebouvier T, Laviña B, Gouveia L, Sun Y, Raschperger E, Räsänen M, Zarb Y, Mochizuki N, Keller A, Lendahl U, Betsholtz C.

Nature. 2018 Feb 22;554(7693):475-480. doi: 10.1038/nature25739. Epub 2018 Feb 14.


Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis.

Falcão AM, van Bruggen D, Marques S, Meijer M, Jäkel S, Agirre E, Samudyata, Floriddia EM, Vanichkina DP, Ffrench-Constant C, Williams A, Guerreiro-Cacais AO, Castelo-Branco G.

Nat Med. 2018 Dec;24(12):1837-1844. doi: 10.1038/s41591-018-0236-y. Epub 2018 Nov 12.