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Available services

Library preparation

  • Single-cell 3´RNA-seq library preparation using 10x Chromium system (v3.1) (10X Genomics - sc mRNAseq).
    Suitable for high throughput single cell transcriptome analysis (several 1000s of cells or nuclei per library) with detection of up to 2000 genes per cell. Full length mRNA information is not preserved.
  • Single-cell 3´RNA-seq library preparation using 10x Chromium system (v3.1) + Cell-surface protein detection (10X Genomics - Feature Barcoding/ CITEseq).
    Bimodal single cell analysis through the combination of transcriptome analysis (several 1000s of cells or nuclei per library) with expression analysis of cell surface markers (pre-defined by user).

    Cell hashing may be useful to partially compensate for technical variability between samples processed simultaneously as well as to combine several low-input samples in one reaction. Full length mRNA information is not preserved.
  • Single-cell ATAC-seq library preparation using 10x Chromium system (v1.1) (10X Genomics - scATAC).
    Suitable for high throughput epigenomic analysis (several 1000s of nuclei per library) at single cell resolution to infer cellular heterogeneity based on accessible chromatin structures.
  • Full-length mRNA-seq library preparation using the iCell8cx (Takarabio - SMARTer).
    Medium throughput (up to 1500) single cell transcriptome analysis providing high gene detection (up to 10 000 genes per cell) as well as accessing the entire length of captured transcripts. Suitable to study for example splice variants or gene fusions. Imaging combined with live-dead staining provides stringent quality control to strictly exclude dead and/ or multiple cells from analysis. 

Next-Generation Sequencing

Libraries are sequenced using NovaSeq6000 or NextSeq500

Computational support

All 10x Chromium-based services include a final report containing a Cellranger web summary file for quality control (QC) of the sequencing outcome, as well as basic data visualization, clustering and a gene count matrix containing all single cells or nuclei passing QC.

For full-length mRNA sequencing on iCell8cx, the final report will include a summary based on Takara’s Hanta pipeline including information such as read and gene count per cell, ribosomal and mitochondrial reads per cell as well as initial cell clustering based on t-distributed stochastic neighbor embedding (t-SNE).

Usage of reporter genes need to be specified before project start and exact sequence information needs to be deposited to be included during sequencing read alignment.

The standard computational service is free of charge and applies to studies carried out in mouse and human samples.

Applications under development

  • Single-cell immune profiling using 10x Chromium system (late-stage development) (10X Genomics - scImmune profiling)
  • Single-cell RNA-seq of full-length mRNA using Smart-seq2 on liquid handling system (early-stage development) (Smart-seq2)
  • MARS-seq (late-stage development) (MARS-seq)

Once we have received the information stated above, we will get back to you within five workdays with a feedback on your request, including a feasibility assessment as well as information on pricing and sample deposition if applicable.

Page Manager:

Contact for service:

    SingleCell [dot] CTGservice [at] med [dot] lu [dot] se
    Phone: +46730968048

    Julia Bräunig
    Ulrich Pfisterer

    Julia Bräunig

    Contact CTG:  

       Phone: +46706855137 
       E-mail: CTGservice [at] med [dot] lu [dot] se

    Visiting Addresses:

       Medicon Village 404:B3                                BMC - Biomedical Centre
       Scheelevägen 2                                             Sölvegatan 23 B
             SE-223 81 Lund                                             SE - 221 85 Lund

             Link to map for Medicon Village                  Link to map for BMC