Single-Cell and Spatial Genomics Platform

General guidelines

Consultations and Service Projects, as well as a Booking Schedule are available in iLab (see “How to start a project”)

Gentle sample isolation is essential to prevent bias against vulnerable cell types while fast isolation is desirable to reduce degradation of nucleic acids.

Thus, prior to initiating a project at the Single-Cell Genomics Platform, users are asked to thoroughly evaluate a cell or nucleus isolation strategy suitable for their target tissue and research question. Users are also strongly encouraged to evaluate their sample quality (e.g. RNA integrity) prior to submitting single-cell genomics work at the facility.

Once a project is accepted by the Single-Cell Genomics Platform, users must follow sample preparation and delivery instructions provided by the platform.

Available services

scTranscriptomics

• Single-cell Gene Expression (3´GEX) library preparation (10x Genomics, v3.1, scmRNAseq)
  • CITE-Seq
  • Hashing
  • CRISPR Screen
• Single-cell Immune Profiling library preparation (10x Genomics, v2, scVDJ)
  • Full-length TCR/BCR sequences
  • Feature Barcode
• Single-cell Multiome ATAC + Gene Expression (10x Genomics, scMultiome)

scTranscriptomics (fixed cells/nuclei)

• Single-cell Gene Expression Flex Profiling (10x Genomics, v.1, Flex, custom probe design)
  • Cell Surface Protein
• Evercode™ WT (Parse Bioscience, Parse)

scEpigenomics

• Single-cell ATAC-seq library preparation (10x Genomics, v2,  scATAC)
• Single-cell Multiome ATAC + Gene Expression (10x Genomics, scMultiome) 

Cell isolation

• High precision cell isolation of sparse biological samples using CellenOne F1.4.

Spatial transcriptomics

• Spatial transcriptomics on FFPE fixed specimen using Visium CytAssist

Computational support

Our single-cell pipeline can be found in our organizations github at https://github.com/ctg-lund/singleCellWorkflows where you can find our up-to-date automated workflows and their documentation.

All 10x Genomic services include a final report containing a Cell Ranger web summary file for quality control (QC) of the sequencing outcome, as well as FASTQ, BAM, gene count matrix containing all single cells or nuclei passing QC, basic visualization and clustering. The standard output also includes a .cloupe file for exploring your samples with the 10x Loupe browser for each sample individually as well as for multiple samples as aggregated data.  

Usage of reporter genes need to be specified in iLab before project start and the exact sequence information and gene co-ordinates need to be submitted to be included during sequencing read alignment.

The standard computational service is free of charge.

Equipment

• 10x Genomics Chromium Controller
• 10x Genomics Chromium X
• Scienion CellenOne F1.4  
• Nexcelom Cellaca Mx
• Illumina Sequencer NovaSeq 6000, NextSeq 2000, NovaSeq X Plus

Applications under development

• Single-cell proteomics using the proteochip on the CellenOne F1.4.
• Customization of existing 10x Genomics applications (e.g. DogmaSeq, viral barcode capturing, integration with long-read technology using Oxford Nanopore).

If you are interested in collaborating with us for our protocols under development, or if you have a suggestion for the implementation or development of a novel method, please contact Julia Bräunig (singlecell [dot] ctgservice [at] med [dot] lu [dot] se (singlecell[dot]ctgservice[at]med[dot]lu[dot]se)).