Eukaryotic Single Cell Genomics

Infrastructure Unit

Recent user publications

The publications in this database are the result of research conducted at the units of SciLifeLab – both in user projects and technology development.


Rickard Sandberg, Platform Scientific Director

Sten Linnarsson, Co-Founder


Anastasios Glaros, Bioinformatician

Helena Parra Acero, Research Specialist

Michelle Ljungmark, Research Engineer

Samaneh Masoumi, Research Engineer

Henrik Gezelius, Research Engineer (on leave)

Karolina Wallenborg, Research Specialist (on leave)


Eukaryotic Single Cell Genomics

Single-cell genomics 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) unit 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


  • scRNA-seq
  • snRNA-seq
  • scATAC-seq
  • Multiome: scRNA-seq + scATAC-seq
  • scCut&Tag
  • Immune profiling: GE + V(D)J
  • CITE-seq
  • Multiplexing with cell hashing and Cellplex
  • Single-cell CRISPR screening in collaboration with the HTGE unit
  • Sequencing: We sequence our single-cell libraries with NGI Stockholm
  • Bioinformatics; We refer to NBIS for project specific bioinformatic analysis.

We can run single-cell genomics projects that require biosafety level 3 (airborne) in collaboration with the BSL3 unit at Biomedicum, KI. Contact us for more information.

Using the unit

For questions or inquiries about new or ongoing projects, please send us an email to :


Single-Cell RNA-sequencing/Single-Nucleus RNA-sequencing

  • Smart-seq3, full-length RNA-sequencing (w/ 5′ UMI) in 384 well plates
  • Smart-seq2, full-length RNA-sequencing (being phased-out).
  • Full-length transcriptome analysis, ICELL8 cx/TAKARA
  • 10XGenomics, droplet-based, 3′ Gene Expression

Single-Cell ATAC-sequencing/Single-Cell Cut&Tag

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
  • Mantis low volume liquid dispenser, Formulatrix
  • VICTORNivo-Multimode Plate Reader, Perkin Elmer

Mailing Address

ESCG, Gamma4
Box 1031
171 21 Solna

Visiting Address

ESCG, Gamma 4
Tomtebodavägen 23A
171 65 Solna

Last updated: 2023-01-18

Content Responsible: Scilifelab Administration()