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.

Booking system
Alternative text: "Illustration for the scOpenLab, featuring microscopic images of cells, highlighting the single-cell research focus of the DKFZ Open Lab initiative."

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.

Instrumentation

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.

Illumina Single Cell 3' RNA  (https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/single-cell-rna-prep.html)

Bead-based but microfluidics free workflow for generating 3' single-cell RNA-seq libraries. Cells and barcoding beads are mixed via several vortexing steps and RNA is eventually barcoded in a gel. 

 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. 

Combinatorial barcoding

Cells or nuclei can also be used a reaction compartments to barcode RNA in a cell-unique fashion. Two workflows are established in the scOpenLab from parse biosciences and scale biosciences (now part of 10X Genomics).

https://www.parsebiosciences.com/

https://scale.bio/

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.

Available readouts

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 barcodes positioned in 2x2 µm squares. Close-to single cell resolution can be achieved with additional stainings such H&E or immunofluorescence. All steps including optimization, imaging, Cytassist transfer and library preparation can be done in our spatial lab with our guidance. 

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 480 transcripts in fresh frozen and FFPE samples with various options for panel customization. Signal amplification via a rolling circle reaction allows the analysis of isoforms or fusions. Also 5000 genes 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. 

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. 

How to get started

1)   Visit our introductory seminar

For all new users we offer a single-cell sequencing and spatial omics 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:

  • 01.12.2026    9:30 - 11:00 AM   TP3 1.OG Raum B1.301        - Single cell sequencing & Spatial omics   Please register here (event 1741).
  • 20.01.2027  13:00 - 14:30 AM   TP3 4.OG Raum B4.101         - Single cell sequencing & Spatial omics   Please register here (event 1742).
  • 23.02.2027  10:00 - 11:30 AM   TP3 4.OG Raum B4.101         - Single cell sequencing & Spatial omics   Please register here (event 1743).
  • 13.04.2027  10:00 - 11:30 AM   TP3 4.OG Raum B4.101         - Single cell sequencing & Spatial omics   Please register here (event 1744).

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

  • Employee image

    Katharina Bauer

  • Employee image

    Dr. Pooja Sant

  • Employee image

    Laura Giese

  • Employee image

    Denise Keitel

  • Employee image

    Dr. Michele Bortolomeazzi

  • Employee image

    Dr. Cindy Pamela Ulloa Guerrero

  • Employee image

    Laura Schütze

  • Employee image

    Dr. Jan-Philipp Mallm

Selected Publications

Cancer Discov. 2026.

Zhang X, Kamiyama M, Tulessin M, Rinck L, Mallm JP, Kilian M, Agardy DA, Heikenwälder M, Platten M, Mogler C, Singhal M, Augustin HG.

Nat Commun. 2026.

Pribus SJ, Osredek I, Otoničar J, Simovic-Lorenz M, Giovenino C, Rademacher A, Wille SJ, Berzain Battioni C, Scherer M, Manzano-Sanchez S, Kienzle A, Parekh U, Villacorta L, Benes V, Sant P, Mallm JP, Brand K, Rippe K, Riemer AB, Sültmann H, Plass C, Stankovic M, Korbel JO, Rausch T, Ernst A.

Cancer Cell. 2026.

Jassowicz L, Feng F, Warta R, Heinicke F, Wöllner A, Briesch H, Sor F, Soller J, Lotsch C, Wong JKL, Park CG, Aubert N, Scheer M, Hu Z, Knoll M, Schlegel J, Frank L, Dao Trong P, Jungwirth G, Nohman AI, Maaß K, Grabe N, Barthel M, Butz S, Lulay C, Zucknick M, Bortolomeazzi M, Sant P, Thewes V, Michel L, Fremd C, Schneeweiss A, Sun C, Rippe K, Abdollahi A, von Deimling A, Unterberg A, Krieg SM, Mallm JP, Lichter P, Zapatka M, Seiffert M, Herold-Mende C.

Nat Genet. 2026.

Maas SLN, Tang Y, Stutheit-Zhao E, Rahmanzade R, Blume C, Hielscher T, Zettl F, Benfatto S, Calafato D, Sill M, Benotmane JK, Yabo YA, Behling F, Suwala A, Kardo H, Ritter M, Peyre M, Sankowski R, Okonechnikov K, Sievers P, Patel A, Reuss D, Friedrich MJ, Stichel D, Schrimpf D, Van den Bosch TPP, Beck K, Wirsching HG, Jungwirth G, Hanemann CO, Lamszus K, Etminan N, Unterberg A, Mawrin C, Remke M, Ayrault O, Lichter P, Reifenberger G, Platten M, Kacprowski T, List M, Pauling JK, Baumbach J, Milde T, Grossmann R, Ram Z, Ratliff M, Mallm JP, Neidert MC, Bos EM, Prinz M, Weller M, Acker T, Hartmann FJ, Preusser M, Tabatabai G, Herold-Mende C, Krieg SM, Jones DTW, Pfister SM, Wick W, Kalamarides M, von Deimling A, Heiland DH, Hovestadt V, Gerstung M, Schlesner M ; German “Aggressive Meningiomas” Consortium (KAM) ; Sahm F.

Nature. 2026.

Li X, Lebeaupin C, Kadianaki A, Druelle-Cedano C, Vesper N, Rennert C, Huguet-Pradell J, Gomez Ramos B, Fan C, Piecyk RS, Zizmare L, Ramadori P, Li L, Frick L, Qiu M, Zhang C, Martins Nascentes Melo L, Ranvir VP, Shen P, Hanselmann J, Kosla J, Fernández-Vaquero M, Vucur M, Baskaran P, Bao X, Coleman OI, Tang Y, Cetin M, Chen Z, Jang I, Del Prete S, Rahbari M, Zhang P, Pham TV, Hou Y, Sun A, Gu L, Kim LC, Rothermel U, Heide D, Ali A, Gallage S, Talvard-Balland N, Piqué-Gili M, Gris-Oliver A, Bevilacqua A, Schlicker L, Duffey A, Unger K, Szydlowska M, Hetzer J, Odom DT, Machauer T, Bucci D, Sant P, Lee JH, Rösler J, Meckelmann SW, Schreck J, Murray S, Simon MC, Nahnsen S, Schulze A, Ho PC, Jugold M, Breuhahn K, Mallm JP, Schirmacher P, Roth S, Rahbari N, Tschaharganeh DF, Roessler S, Goeppert B, Bengsch B, Andrieux G, Boerries M, Malek NP, Prinz M, Weber A, Zeiser R, Tamayo P, Bronsert P, Kurowski K, Thimme R, Yuan D, Carretero R, Luedde T, Pinyol R, Hartmann FJ, Karin M, Tasdogan A, Trautwein C, Mall M, Hofmann M, Llovet JM, Haller D, Kaufman RJ, Heikenwälder M.

Links

Booking system
NFDI4Bioimage
Initiative for FAIR spatial data (IO-FAST)

Get in touch with us

Employee image

Dr. Jan-Philipp Mallm

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