Eukaryotic Single Cell Genomics

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.


  • Smart-seq2: Full length transcript sequencing (50bp, single read)
    Format: User FACS dispense cells/nuclei into 384 well plates containing lysis buffer. ESCG process these plates through reverse transcription, PCR, QC of cDNA, Nextera library preparation, QC of library, sequencing and Smart-seq2 analysis pipeline.
  • STRT-seq-2i: Quantitative 5’ end transcript sequencing (50bp, single read)
    Format: Cells/Nuclei suspensions stained with fluorescent dye are dispensed by limiting dilution into Customized 9600 well chip array at ESCG. Imaging is performed and reverse transcription and PCR only takes place in wells where single cells are identified. cDNA is pooled and QC, followed by library preparation, QC of library, Sequencing and STRT-seq- 2i analysis pipeline.
  • 10XGenomics - Drop-seq: Quantitative 3’ end transcript sequencing (100bp, pair-end)
    Format: Cells/Nuclei suspensions are encapsulated into droplets using the 10X Chromium controller, followed by cDNA synthesis and library preparation as described for the Chromium Single Cell 3’ Reagent kit v2. QC at both stages of cDNA and Library preparation are performed. Sequencing data is run through the Cell Ranger analysis pipeline.


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


  • Nikon ECLIPSE Ti-E inverted microscope system
  • TECAN EVO liquid handling robotic system, 96 & 384 head
  • NanoDrop, low volume liquid dispenser
  • Wafergen, SmartChip Multisample Nanodispenser
  • Chromium, 10XGENOMICS
  • Agilent Bioanalyzer
  • Fragment Analyzer


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

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes
Segerstolpe Å, Palasantza A, Eliasson P, Andersson EM, Andréasson AC, Sun X, Picelli S, Sabirsh A, Clausen M, Bjursell MK, Smith DM, Kasper M, Ämmälä C, Sandberg R.
Cell Metab. 2016 Oct 11;24(4):593-607. doi: 10.1016/j.cmet.2016.08.020. Epub 2016 Sep 22.