Core Facility

Single-cell Open Lab

Dr. Jan-Philipp Mallm

The Single-cell Open Lab provides an infrastructure for processing cells, preparing libraries for single-cell sequencing as well as spatial omics. New users will be trained in most of our workflows so they can perform all experimental steps autonomously in the scOpenLab. We offer regular seminars to introduce new users to our portfolio. Systems can be booked online and a training session / detailed project discussion can be arranged. We also supports setting up new methods in collaborations.

Services

We operate as an open lab which means we teach scientists to run the experiments themselves. Guidance and support is provided at every stage from project planning, optimization, experimental setup and library generation. The technologies we offer are described below, however our portfolio of methods and instruments is constantly being updated and expanded. We continuously develop custom protocols for cancer research and work with many groups at DKFZ and multispace to provide exciting techniques for the single-cell and spatial community. Please get in contact with us, if you either have innovative ideas about new workflows or read-outs. We happy to support the implementation and trouble shooting.

Available readouts

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.

How to get started

1)   Visit our introductory seminar

For all new users we offer a single-cell sequencing seminar covering the different techniques, pros & cons, project design and lab logistics. The introduction is mandatory for all new scOpenLab users.

At the following dates the next mandatory introductions will take place:

  • 16.01.2025    9:30 - 11:00 AM   TP3 B4.101        - Single cell sequencing
  • 13.02.2025    9:30 - 11:00 AM   TP3 B4.101        - Spatial omics

If you would like to participate, please send an e-mail to: scopenlab(at)dkfz.de (subject: introductory seminar).  See you there! 

2)   Make an appointment with us to discuss your project in detail (optional but highly recommended)

3)   Create an account for booking machines online: ppms link. You will also find a collection of protocols and further material on our ppms webpage.

4)   Book machines for your first experiment and request assistance

For all new users we will offer an introduction on an individual basis for each machine / technique in the lab according to their project.

We offer some central chemistry for e.g. optimizations, SMART-seq, barcodes, spatial transcriptomics workflows - please refer to the order section in our booking system.

5)   Run your experiment with a scOpenLab staff member

Team

  • Katharina Bauer

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  • Dr. Pooja Sant

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  • Laura Giese

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  • Denise Keitel

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  • Dr. Michele Bortolomeazzi

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  • Dr. Afzal Pasha Syed

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  • Dr. Jan-Philipp Mallm

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Selected Publications

Nat Commun. 2025.
Dev Cell. 2025.
Genome Biol. 2024.
Nat Commun. 2024.
Nat Commun. 2024.

Get in touch with us

Dr. Jan-Philipp Mallm
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