The Genomics Technology Platform provides support to researchers from the Max Delbrück Center and BIH/Charité and is committed to implement key sequencing technologies and to establish state-of-the-art service pipelines.

We operate Illumina, Oxford Nanopore and PacBio platforms and offer standard as well as customized library preparation workflows to our users.
 

Single-cell multi-omics and spatial biology technologies are a major focus of our work. Our integrated Flow Cytometry unit enables us to select and isolate cells on site. A broad range of state-of-the-art single-cell applications are available for downstream analyses.

We constantly implement novel techniques in collaborative research projects and are closely working with clinical researchers to translate these technologies into systems medicine. By providing a multi-omics view on the pathophysiology of patient or model system samples, we support clinical scientists to delineate the underlying mechanisms of diseases like cancer, cardiovascular events, or neurological disorders.

Contact

Dr. Janine Altmüller

Head of Genomics

Phone:
+49 30 9406 1434
E-mail:
janine.altmueller[at]bih-charite.de

Akkordeon

  • Next Generation Sequencing Team

    Leader Tatiana Borodina
    [email protected]
    Phone: 030 9406 1341 | 030 450 643 367 
    Publications

    We operate an impressive line of sequencing platforms (Illumina, PacBio, Oxford Nanopore), pipetting robots and analytical equipment at our high-throughput sequencing lab at the Rahel-Hirsch-Center. The team has extensive experience implementing novel protocols, automating library preparation, and methodological development.

    Available services and technologies include:

    • Consultations on NGS-related questions;
    • Support in the experimental design of NGS projects;
    • QC for DNA and RNA samples and sequencing libraries;
    • Library preparation from bulk material for diverse -Seq applications:
    • RNA sequencing (e.g. mRNA-, totalRNA-, 3’mRNA-, miRNA-Seq),
    • DNA sequencing (e.g. whole genome, whole exome, amplicon, cfDNA),
    • Epigenome (ChIP-Seq, Methyl-Seq, direct RNA and DNA sequencing);
    • Short-read sequencing on Illumina instruments: iSeq, MiSeq, MiniSeq, NextSeq 2000, NovaSeq 6000, NovaSeq X plus;
    • Long-read sequencing on Pacific Biosciences Revio;
    • Long-read sequencing on Oxford Nanopore MinION and PromethION platforms

    For consulting and assistance in planning of a sequencing experiment please contact us at [email protected] or [email protected].

    Actual pricelist valid for MDC, Charité and BIH users is available upon request. Large-scale projects require individual cost calculation.

    If the service or the protocol you require is not in the pricelist, please contact us. Our official portfolio is limited to the most frequently requested services. We will find a customized solution for you.

    Ordering and Turnaround time

    Services are currently ordered per email to [email protected]  or to [email protected] or to the members of the NGS Unit you are already in contact with.

    Each service project has to be registered by filling the Project Registration Form and a relevant Sample Transfer Form – forms are sent out per email.

    The specific number assigned by the NGS team to each project is used as a reference for further communication.

    Generally, the projects are processed in the order of samples (libraries) receipt.

    Scheduling of sequencing libraries preparation for any platform depends on the current workload and equipment availability.

    Illumina sequencing schedule depends on how fast the samples requiring the same sequencing mode are collected to fill up a flowcell. If you're ready to sequencing libraries occupy the whole flowcell, usually they can be sequenced within 1-2 weeks after the delivery.

    Loading of ready libraries on PacBio and Oxford Nanopore PromethION is also usually possible within 1-2 weeks, depending on the sequencing queue.

  • Single-cell Team

    Leader Thomas Conrad
    thomas.conrad@mdc-berlin.de
    Phone: 030 9406-1481

    The Single-cell technologies team provides access to an exceptionally wide range of cutting-edge single-cell and spatial multiomics approaches in our lab at the Berlin Institute of Medical Systems Biology. . To facilitate easy access for a broad user community, we provide close support from experimental design to sample preparation and data processing. In addition to regular services, we offer individual user training to enable independent access to our advanced instruments. Single-cell technologies are rapidly evolving; we therefore continuously implement novel approaches in the context of collaborative research projects.

    Available services and technologies include:

    • Counseling on study design
    • Counseling on sample preparation
    • Droplet-based approaches (10X Genomics; Dolomite)
    • Plate-based assays (Smart-Seq2/3; G&T-Seq; scBS+T-Seq)
    • Spatial transcriptomics (10X Genomics Visium + Xenium; Nanostring GeoMx + CosMx)

    An increasing number of molecular modalities has become accessible by single-cell genomics in recent years. The resulting molecular signatures provide a comprehensive view on the individual cell types that together form a complex tissue, their functional states and developmental trajectories.

    Eventually, single-cell Multiomics approaches provide a unique opportunity to discover exclusive characteristics of a diseased cell state.

    Available assays include the detection of gene expression profiles, open chromatin regions, DNA sequence, cell surface epitopes, or T- and B- cell receptor sequences, and combinations thereof for thousands of single cells in parallel.

    In addition, spatial transcriptomic approaches allow us to assay individual cells in their spatial context, and reconstruct tissue architecture and its changes in response to environmental cues or in disease states.

    Our integrated Flow Cytometry unit enables us to perform initial quality control of single-cell preparations, and to select and isolate cell populations directly on site for droplet- or plate-based assays. 

    Open access instruments for droplet encapsulation, robotics, and library QC can be booked here: https://iris.mdc-berlin.de/ (Provider Genomics Technollogy Platform).

  • Flow Cytometry Team

    Leader: Caroline Braeuning
    caroline.braeuning@mdc-berlin.de 
    Phone: 030 9406 3043

    Cell sorting and flow cytometric analysis is often a starting point for Genomics and Transcriptomics assays like initial quality control of single-cell preparations or selection of specific cell populations for droplet- or plate-based single cell transcriptomic assays. The FACS team closely collaborates with the Single Cell Technologies team and can therefore provide support with a special focus on Genomics users and their needs. Additionally, all other flow cytometric users are supported and welcome.

    We are equipped with state-of-the-art conventional and spectral instruments: four cell sorters (one BD FACS AriaIII, two BD FACS AriaFusion, one BD FACSDiscover S8) and one analyzer (BD Fortessa X-20 with HTS) in our lab at the Berlin Institute of Medical Systems Biology. 

    All appointments for cell sorting are assisted at an individual level to enable successful experiments for users with varying knowledge levels of flow cytometry. The sorters are available during service hours; the analyzer is flexibly bookable after training and sufficient experience.

    Please contact the team for further information about consultation, training, instrument configuration, pricing and booking at [email protected].

  • Data Management Team

    Leader Marten Jäger
    marten.jaeger@bih-charite.de 
    Phone: 030 450 569 048

    The process of collection and processing of genomic data is still lacking sufficient level of standardisation. To close that gap, our group, located at the Rahel-Hirsch-Center, strives to implement automated software solutions for genomic data processing and analysis enabling effective introduction of quality control measures safeguarding reproducibility.

    Regarding data management issues please contact helpdesk-genomics@charite.de. 

    Please refrain from directly contacting individual members of the data management group to avoid lost inquiries.

  • Team Members

    Bastian Salewsky
    bastian.​salewsky@​bih-​charite.​de
    +49 30 450 643 364 
    RHC lab
    PacBio and Oxford Nanopore sequencing | NGS library preparation | Nucleic acids isolation

    Carola Dietrich
    carola.​dietrich@​mdc-​berlin.​de 
    +49 30 9406 1342
    MDC lab
    Single-cell genomics

    Caroline Braeuning
    caroline.​braeuning@​mdc-​berlin.​de
    +49 30 9406 – 3043
    MDC lab
    Team leader Flow Cytometry

    Catrin Janetzki
    catrin.​janetzki@​bih-​charite.​de
    +49 30 450 643 366  
    RHC lab
    NGS library preparation | Illumina sequencing

    Claudia Quedenau
    quedenau@​mdc-​berlin.​de
    +49 30 450 643 364 
    RHC lab
    Safety and first aid | PacBio and Oxford Nanopore sequencing | NGS library preparation

    Cornelia Schlee
    cornelia.​schlee@​bih-​charite.​de
    +49 30 450 643 366
    RHC lab
    NGS library preparation | Illumina sequencing

    Cornelius Fischer
    cornelius.​fischer@​bih-​charite.​de 
    +49 30 450 569 048
    RHC
    Data management

    David Larrea
    [email protected]  
    BIMSB lab
    Single Cell Technologies

    Elisabeth Kirst
    elisabeth.​kirst@​charite.​de
    +49 30 450 643 365 
    RHC lab
    NGS library preparation | Illumina sequencing

    Erdost Yildiz
    erdost.yildiz@mdc-berlin.de
    +49 30 9406 3043
    MDC lab
    Flow cytometry Senior Lab Manager 

    Helene Pflugk
    helene.pflugk@​mdc-​berlin.​de
    +49 30 9406 1357
    MDC lab
    Flow cytometry support

    Isabell Becker
    isabell.becker@mdc-berlin.de
    +49 30 450 676 272
    RHC lab
    NGS library preparation | Illumina sequencing

    Izabela Plumbom
    izabela.​plumbom@​mdc-​berlin.​de
    +49 30 9406 1320
    MDC lab
    Single-cell genomics | Spatial transcriptomics

    Jakob Hilgenfeld
    jakobhannes.hilgenfeld@mdc-berlin.de
    +49 30 9406 3266
    MDC lab
    student assistent

    Janine Altmüller
    janine.​altmueller@​mdc-​berlin.​de
    janine.​altmueller@​bih-​charite.​de
    +49 30 9406 1434
    +49 30 450 643 363 

    Head of BIH/MDC Genomics Technology Platform

    Jeannine Wilde
    jeannine.​wilde@​mdc-​berlin.​de
    +49 30 450 643 368 
    RHC lab
    Illumina sequencing coordination | NGS library preparation

    Kirsten Richter
    kirsten.​richter@​mdc-​berlin.​de
    Lab administration

    Madlen Sohn
    madlen.​sohn@​mdc-​berlin.​de
    +49 30 450 643 365 
    RHC lab
    NGS library preparation | Illumina sequencing

    Marten Jäger
    marten.​jaeger@​bih-​charite.​de
    +49 30 450 569 048
    RHC
    Team leader Data management

    Michaela Seeger-Zografakis
    mseeger@​mdc-​berlin.​de
    +49 30 9406 1324
    MDC lab
    Flow Cytometry support 

    Namuun Battur
    namuun.​battur@​bih-​charite.​de 
    +49 30 450 669 048
    RHC lab
    Data Management 

    Sarah Vitcetz
    sarah.​vitcetz@​mdc-​berlin.​de
    +49 30 9406 3041
    MDC lab
    Lab management / single cell genomics / spatial transcriptomics 

    Shauna Kehoe
    shauna.kehoe@bih-charite.de
    RHC lab
    Oxford Nanopore sequencing | NGS library preparation

    Sonja Hansen
    sonja.​hansen2@​bih-​charite.​de
    +49 30 450 669 048
    RHC lab
    Scientific Project Coordinator | Einstein Center for Early Disease Interception

    Tatiana Borodina
    tatiana.​borodina@​mdc-​berlin.​de
    +49 30 9406 1341 
    +49 30 450 643 367 
    MDC / RHC
    Team leader Next Generation Sequencing 

    Thomas Conrad
    thomas.​conrad@​mdc-​berlin.​de
    +49 30 9406 1481
    MDC
    Team leader Single-cell Technologies

    Ulrike Krüger
    ulrike.​krueger@​bih-​charite.​de
    +49 30 450 643 507
    RHC lab
    Project coordination and Lab management | NGS library preparation | Illumina sequencing

    Ute Ungethüm
    ute.​ungethuem@​bih-​charite.​de
    +49 30 450 676 272
    RHC lab
    Coordination of large-scale projects (Charité lab) | Automation of nucleic acid extraction and QC assays

    Wassim Salam
    wassim.​salam@​bih-​charite.​de
    +49 30 450 669 048
    RHC lab
    Data management

  • Steering Committee

    BIH
    Christian Conrad
    Stefanie Großwendt
    Ute Scholl

    MDC
    Yo Lee
    Ilaria Piazza
    Nikolaus Rajewsky

    Guests
    Nils Blüthgen (Charité)
    Anton Henssen (MDC/Charité)

Publications