Single-cell sequencing
Chromium system (www.10xgenomics.com)
- scRNA-seq (3' / 5' counting)
- scVDJ-seq (+scRNA-seq)
- scATAC-seq
- multiome kit - RNA+ATAC
- CITE-seq & cell hashing
- numerous sample pooling strategies
- scDNA+RNA-seq (HIPSDR-seq)
- scChIP-seq + RNA-seq
The preparation of a clean single-cell suspension is key for a successful experiment. We can provide protocols / guidelines for dissociation, nuclei extraction from frozen tissue and nuclei preparation for scATAC-seq. All cell / nuclei suspensions can be analyzed with an automated cell counting system at the scOpenLab prior to loading.
Tapestri (www.missionbio.com)
- targeted scDNA-seq
- SDR-seq
- protein + DNA-seq
For targeted single-cell sequencing we can provide access to the Tapestri (scDNA-seq) system. Panels for targeted amplification can be designed or directly purchased from the companies - for further information please visit their websites.
Automized on plates
- scRNA-seq (SMART-seq 2.5, muta-seq and others)
- scHiC
- scWGBS
- G&T-seq
- scNMT-seq
- scWGS / scWES (PTA)
Automated workflows are conducted with the Bravo, Mosquito, C.wash and Mantis systems, depending on the reaction volume. Customized protocols can be programmed and run on all machines and we are happy to work with you for setting up those protocols.
Spatial transcriptomics
RNAscope HiPlex Assay
We offer test chemistry, guidance and experimental support for HiPlex Assays. Both fresh frozen und FFPE samples can be analysed with pre-defined targeted FISH probes and single-cell resolution. Staining and imaging equipment is available via our booking system.
10x Genomics Visium slide
While RNAscope provides single-cell resolution for up to 48 different pre-defined targets, visium sildes cover the whole transcriptome using spotted barcodes with a diameter 55 µm or with 2x2 µm square in case of visium HD. All steps including optimization, imaging, Cytassist transfer and library preparation can be done in our spatial lab.
Merfish
Merfish enables users to detect up to 960 transcripts in fresh frozen and FFPE samples. Subsequent antibody readouts can be performed for five protein targets using prelabeled secondary antibodies.
Xenium
The Xenium chemistry can detect up to 400 transcripts in fresh frozen and FFPE samples. Signal amplification via a rolling circle reaction allows the analysis of isoforms or fusions. Also 5k panels can be run on our system.
Spatial proteomics
COMET by Lunaphore
We offer training and test antibodies to familiarize users with the seqIF workflow. Both fresh frozen und FFPE samples can be analysed. Staining and imaging is performed automatically by the system after successful panel optimization.
MACSima by Miltenyi
The MACSima allows detection of over 100 proteins via directly labelled antibodies. The fluorophore is either bleached or removed using the REAdye technology.
Each methodology has its merits (apart from the number of transcripts / proteins). If you are lost in space, we are happy to provide guidance in selecting the best technology for your project. Please discuss your spatial projects at an early stage with us - please do not order anything prior to a project discussion!
