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



  • Single cell RNA-sequencing
  • Single nucleus RNA-sequencing
  • Single cell ATAC-sequencing
  • Single cell immune profiling
  • Bioinformatics; We refer to NBIS for project specific bioinformatic analysis.



Single Cell RNA-sequencing/Single Nucleus RNA-sequencing

  • Smart-seq2, full-length RNA-sequencing. More info
  • 10XGenomics, 3' gene expression. More info.
  • STRT-seq 2i, 5' gene expression. More info.
  • Full-length transcriptome analysis, ICELL8 cx/TAKARA

Single Cell ATAC-sequencing

Single Cell Immune profiling

  • V(D)J, gene expression and cell surface protein expression from the same cell. More info


  • 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, 10XGENOMICS
  • Bioanalyzer, Agilent
  • Fragment Analyzer, Agilent


Multipotent peripheral glial cells generate neuroendocrine cells of the adrenal medulla

Furlan A, Dyachuk V, Kastriti ME, Calvo-Enrique L, Abdo H, Hadjab S, Chontorotzea T, Akkuratova N, Usoskin D, Kamenev D, Petersen J, Sunadome K, Memic F, Marklund U, Fried K, Topilko P, Lallemend F, Kharchenko PV, Ernfors P, Adameyko I.

Science. 2017 Jul 7;357(6346). pii: eaal3753. doi: 10.1126/science.aal3753


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.


Neuronal heterogeneity and stereotyped connectivity in the auditory afferent system.

Petitpré C, Wu H, Sharma A, Tokarska A, Fontanet P, Wang Y, Helmbacher F, Yackle K, Silberberg G, Hadjab S, Lallemend F.

Nat Commun. 2018 Sep 12;9(1):3691. doi: 10.1038/s41467-018-06033-3.


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.