Single-cell Open Lab (scOpenLab)

Single cell sequencing (sc-seq) technologies are evolving fast and become more and more important for many research groups at the DKFZ. The scOpenLab offers assisted access to instrumentation for processing cells and preparing the libraries for sc-seq as well as spatial transcriptomics to all DKFZ groups.

The lab is headed by Jan-Philipp Mallm (j.mallm@dkfz.de) and is located in the Bioquant in rooms 423-425 on the 4th floor.

We offer regular seminars (please see below) to introduce new users to single-cell sequencing and spatial applications. After participating in the seminar the systems can be booked online and a training session / detailed project discussion can be arranged.

The scOpenLab also supports setting up new protocols or developing new methods in collaboration with research groups. Here, we focus on providing automated, high-throughput and multi-omic readouts tailored to cancer research.

To obtain spatially resolved transcriptome data we currenly offer five workflows in the new spatial lab.

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. All steps including optimization, imaging and library preparation can be done in our spatial lab. Cytassist workflows are also supported.

Molecular cartograhy

Molecular Cartography is a multiplex spatial analysis that allows the detection of up to 100 transcripts in intact tissue. Further readouts that complement the cyclic FISH signal can be recorded, such as H&E or protein IF.

Merfish

Merfish enables users to detect up to 500 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.

Each methodology has its merit (apart from the number of transcripts). If you are lost in space, we are happy to provide guidance in selecting the best technology for your project.  

We are happy to discuss your spatial projects - please do not order anything prior to a project discussion!

To obtain spatially resolved proteomics data we currenly offer two workflows

1) 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. 

2) Mibiscope by Ionpath

The MIBIscope allows the detection of over 40 markers simultaneously using single step imaging. The antibody based approach uses secondary ion mass spectrometry and thus requires labelling with elemental mass tags. To detect the tags the systems releases the secondary ions via a primary charged ion beam.  

1)   Visit our introductory seminar

For all new DKFZ 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 (seminar room Bioquant, ground floor):

• 06.08.2024    10 - 11:30 AM      Bioquant SR042 - Single cell sequencing
• 12.09.2024    10 - 11:30 AM      Bioquant SR042 - Spatial omics
• 17.10.2024    10 - 11:30 AM      Bioquant SR042 - Single cell sequencing
• 21.11.2024    10 - 11:30 AM      Bioquant SR042 - Spatial omics

If you would like to participate, please send an e-mail to: scopenlab@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

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

Jan-Philipp Mallm

Katharina Bauer

Denise Keitel

Laura Giese

Pooja Sant

Afzal Syed

Michele Bortolomeazzi

Alik Huseynov 

scOpen Lab (W192)
Bioquant Center, room 423
Im Neuenheimer Feld 267
69120 Heidelberg
Germany
Tel.: +49-6221-54-51322 (lab)
Tel.: +49-6221-54-51378 (office)
e-mail: scOpenLab@dkfz.de

https://mastodon.social/@scopenlab

NFDI (https://nfdi4bioimage.de/en/start/)

DFG (https://www.dfg.de)

Ghasemi DR, Okonechnikov K, et al. Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage. Nat Commun. 15:269 (2024), doi: 10.1038/s41467-023-44117-x

Schuster, LC. et al. Progenitor-like cell type of an MLL-EDC4 fusion in acute myeloid leukemia. Blood Adv, 7:7079-7083 (2023), doi: 10.1182/bloodadvances.2022009096.

Piroeva, KV. et al. Nucleosome repositioning in chronic lymphocytic leukaemia. Genome Res, 33:1649-1661 (2023), https://doi.org:10.1101/gr.277298.1229

Wong, J.K.L. et al. scSNPdemux: a sensitive demultiplexing pipeline using single nucleotide polymorphisms for improved pooled single-cell RNA sequencing analysis. BMC Bioinformatics, 24:325 (2023). https://doi.org:10.1186/s12859-023-05440-8

Sant, P., Rippe, K. & Mallm, J. P. Approaches for single-cell RNA sequencing across tissues and cell types. Transcription, 1-19 (2023). https://doi.org:10.1080/21541264.2023.2200721

Poos, A. M. et al. Resolving therapy resistance mechanisms in multiple myeloma by multi-omics subclone analysis. Blood (2023). https://doi.org:10.1182/blood.2023019758

Muckenhuber, M. et al. Epigenetic signals that direct cell type-specific interferon beta response in mouse cells. Life Sci Alliance 6 (2023). https://doi.org:10.26508/lsa.202201823

John, L. et al. Resolving the spatial architecture of myeloma and its microenvironment at the single- cell level. Nat Commun 14, 5011 (2023). https://doi.org:10.1038/s41467-023-40584-4

Sole-Boldo, L. et al. Differentiation-related epigenomic changes define clinically distinct keratinocyte cancer subclasses. Molecular systems biology 18, e11073 (2022). https://doi.org:10.15252/msb.202211073

Montserrat-Vazquez, S. et al. Transplanting rejuvenated blood stem cells extends lifespan of aged immunocompromised mice. NPJ Regen Med 7, 78 (2022). https://doi.org:10.1038/s41536-022- 00275-y

Hageb, A. et al. Reduced adhesion of aged intestinal stem cells contributes to an accelerated clonal drift. Life Sci Alliance 5 (2022). https://doi.org:10.26508/lsa.202201408

Bogeska, R. et al. Inflammatory exposure drives long-lived impairment of hematopoietic stem cell self-renewal activity and accelerated aging. Cell Stem Cell 29, 1273-1284 e1278 (2022). https://doi.org:10.1016/j.stem.2022.06.012

Tirier, S. M. et al. Subclone-specific microenvironmental impact and drug response in refractory multiple myeloma revealed by single-cell transcriptomics. Nat Commun 12, 6960 (2021). https://doi.org:10.1038/s41467-021-26951-z

Reich, M. et al. Downregulation of TGR5 (GPBAR1) in biliary epithelial cells contributes to the pathogenesis of sclerosing cholangitis. J Hepatol 75, 634-646 (2021). https://doi.org:10.1016/j.jhep.2021.03.029

Pfister, D. et al. NASH limits anti-tumour surveillance in immunotherapy-treated HCC. Nature 592, 450-456 (2021). https://doi.org:10.1038/s41586-021-03362-0

Dudek, M. et al. Auto-aggressive CXCR6(+) CD8 T cells cause liver immune pathology in NASH. Nature 592, 444-449 (2021). https://doi.org:10.1038/s41586-021-03233-8