Single-cell Open Lab (scOpenLab)
Overview
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.
Available sc-seq readouts
single-nuclei sequencing
© dkfz.de
Currently, the technologies described below are available. Our portfolio of methods and instruments is constantly being updated and expanded in close interactions with the DKFZ groups of the sc-seq@dkfz network. Please contact us if you miss methods important for your work.
10x Genomics Chromium system (www.10xgenomics.com)
- scRNA-seq (3' / 5' counting)
- scVDJ-seq (+scRNA-seq)
- scATAC-seq
- multiome kit - RNA+ATAC
- CITE-seq & cell hashing
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.
Encapsulation of cardiomyocytes
© dkfz.de
Tapestri (www.missionbio.com)
- targeted scDNA-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.
Single-cell printing
© dkfz.de
Automized on plates
- scRNA-seq (SMART-seq 2.5, muta-seq and others)
- scHiC
- scWGBS
- G&T-seq
- scNMT-seq
- scDNA (PTA)
Automated workflows are conducted with the Bravo (Agilent) or the Mosquito (STP Labtech) systems, depending on the reaction volume. Customized protocols can be programmed and run on both machines and we are happy to work with you for setting up those protocols.
Antibody-free cell hashing
© dkfz.de
- Antibody-free hashing
- Target-sequencing for e.g. mutation calling
- scATAC-seq on 384-well plates
- (multi)-omics by combinatorial barcoding
- more are currently in validation
- scChIP-seq
We continously develop custom protocols for cancer research and work with many groups at DKFZ to provide exciting techniques for the DKFZ single-cell community. Please get in contact with us, if you either have innovative ideas about new workflows or read-outs. We happy to support testing and the implementation.
Spatial transcriptomics
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.
Spatial proteomics
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.
How to get started
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):
- 05.12.2023 10 - 11:30 AM Bioquant SR044 - Spatial omics
- 09.01.2024 10 - 11:30 AM Bioquant SR043 - Single cell sequencing
- 13.02.2024 10 - 11:30 AM Bioquant SR043 - Spatial omics
- 12.03.2024 10 - 11:30 AM Bioquant SR043 - Single cell sequencing
- 23.04.2024 10 - 11:30 AM Bioquant SR043 - Spatial omics
- 04.06.2024 10 - 11:30 AM Bioquant SR043 - Single cell sequencing
- 02.07.2024 10 - 11:30 AM Bioquant SR043 - 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 and more - please refer to the order section in our booking system.
5) Run your experiment with a scOpenLab staff member
Staff members
Jan-Philipp Mallm
Katharina Bauer
Denise Keitel
Pooja Sant
Afzal Syed
Michele Bortolomeazzi
Alik Huseynov
Contact
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
Partners & Funding
DKFZ-HIPO (https://www.dkfz.de/en/hipo/)
Human Cell Atlas (https://www.humancellatlas.org/)
DFG (https://www.dfg.de)
Selected Publications
Roider T, Seufert J, Uvarovskii A, Frauhammer F, Bordas M, Abedpour N, Stolarczyk M, Mallm JP, Herbst SA, Bruch PM, Balke-Want H, Hundemer M, Rippe K, Goeppert B, Seiffert M, Brors B, Mechtersheimer G, Zenz T, Peifer M, Chapuy B, Schlesner M, Müller-Tidow C, Fröhling S, Huber W, Anders S, Dietrich S. (2020) Dissecting intratumour heterogeneity of nodal B-cell lymphomas at the transcriptional, genetic and drug-response levels. Nat Cell Biol, 22:896-906.
Vu T, Straube J, Porter AH, Bywater M, Song A, Ling V, Cooper L, Pali G, Bruedigam C, Jacquelin S, Green J, Magor G, Perkins A, Chalk AM, Walkley CR, Heidel FH, Mukhopadhyay P, Cloonan N, Gröschel S, Mallm JP, Fröhling S, Scholl C, Lane SW. (2020) Hematopoietic stem and progenitor cell-restricted Cdx2 expression induces transformation to myelodysplasia and acute leukemia. Nat Commun,11:3021.
Solé-Boldo L, Raddatz G, Schütz S, Mallm JP, Rippe K, Lonsdorf AS, Rodríguez-Paredes M, Lyko F. (2020) Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming. Commun Biol, 3:188.
Wierzbinska JA, Toth R, Ishaque N, Rippe K, Mallm JP, Klett LC, Mertens D, Zenz T, Hielscher T, Seifert M, Küppers R, Assenov Y, Lutsik P, Stilgenbauer S, Roessner PM, Seiffert M, Byrd J, Oakes CC, Plass C, Lipka DB. (2020) Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL. Genome Med, 12:29.
Delacher M, Imbusch CD, Hotz-Wagenblatt A, Mallm JP, Bauer K, Simon M, Riegel D, Rendeiro AF, Bittner S, Sanderink L, Pant A, Schmidleithner L, Braband KL, Echtenachter B, Fischer A, Giunchiglia V, Hoffmann P, Edinger M, Bock C, Rehli M, Brors B, Schmidl C, Feuerer M. (2020) Precursors for Nonlymphoid-Tissue Treg Cells Reside in Secondary Lymphoid Organs and Are Programmed by the Transcription Factor BATF. Immunity. 52:295-312.
Mallm JP, Windisch P, Biran A, Gal Z, Schumacher S, Glass R, Herold-Mende C, Meshorer E, Barbus M, Rippe K. (2020) Glioblastoma initiating cells are sensitive to histone demethylase inhibition due to epigenetic deregulation. Int J Cancer, 146:1281-1292.
Sacma M, PospiechJ , Bogeska R, de Back W, Mallm JP, Sakk V, Soller K , Marka GM, Vollmer A, Karns R, Cabezas-Wallscheid N, Trumpp A, Mendez-Ferrer S, Milsom M , Mulaw MA , Geiger H, Florian MC. (2019) Haematopoietic stem cells in perisinusoidal niches are protected from ageing. Nat Cell Biol, 21, 1309-1320.
Tirier SM, Park J, Preusser F, Amrhein L, Gu Z, Steiger S, Mallm JP, Waschow M, Eismann B, Gut M, Gut IG, Rippe K, Schlesner M, Theis F, Fuchs C, Ball, CR, Glimm H, Eils R, Conrad C. (2019) Pheno-seq – linking visual features and gene expression in 3D cell culture systems. Scientific Rep, 9:12367
Mallm JP, Iskar M, Ishaque N, Klett LC, Kugler SJ, Muino JM, Teif VB, Poos AM, Großmann S, Erdel F, Tavernari D, Koser SD, Schumacher S, Brors B, König R, Remondini D, Vingron M, Stilgenbauer S, Lichter P, Zapatka M, Mertens D, Rippe K. (2019) Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks. Mol Syst Biol 15:e8339
Becker H, Greve G, Kataoka K, Mallm JP, Duque-Afonso J, Ma T, Niemöller C, Pantic M, Duyster J, Cleary ML, Schüler J, Rippe K, Ogawa S, Lübbert M. (2019) Identification of enhancer of mRNA decapping 4 as a novel fusion partner of MLL in acute myeloid leukemia. Blood Adv 3:761-765.
Kalamakis G, Brüne D, Ravichandran S, Bolz J, Fan W, Ziebell F, Stiehl T, Catalá-Martinez F, Kupke J, Zhao S, Llorens-Bobadilla E, Bauer K, Limpert S, Berger B, Christen U, Schmezer P, Mallm JP, Berninger B, Anders S, Del Sol A, Marciniak-Czochra A, Martin-Villalba A. (2019) Quiescence Modulates Stem Cell Maintenance and Regenerative Capacity in the Aging Brain. Cell 176:1407-1419.