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 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 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

 

InDrop (www.1cell-bio.com)

  • scRNA-seq (3' counting)
  • Custom scRNA-seq drop-seq assays
  • Cell types with unusual size

 Tapestri (www.missionbio.com)

  • targeted scDNA-seq

 

Customized scRNA-seq assays can be conducted with the inDrop system from 1CellBio. 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
  • scHiC
  • scWGBS
  • G&T-seq
  • scNMT-seq

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

 Custom protocols scOpen Lab

  • 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

 

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 two 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.

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:

  • 18.08.2021   10 - 11:30 AM       Virtual meeting
  • 21.09.2021   10 - 11:30 AM       Virtual meeting
  • 26.10.2021   10 - 11:30 AM       Virtual meeting

If you would like to participate, please send an e-mail to: scopenlab@dkfz.de (subject: introductory seminar). You will then receive a zoom link to join the seminar. 

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

3)   Create an account for booking machines online: https://dkfzppms.inet.dkfz-heidelberg.de/scopenlab/

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

Dr. Jan-Philipp Mallm

Katharina Bauer

Dr. Pooja Sant

Laura Giese

Janine Rückheim

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

 

Partners & Funding

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.

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