Core Unit Genomics
Over the past decade, Next Generation Sequencing (NGS) technologies have revolutionized biomedical research.
The BIH / MDC Genomics Technology Platform offers professional project counseling, (single-cell-) library preparation, and sequence production support for all BIH/Charité und MDC users.
Please inform yourself about our terms and conditions if you plan to make use of our services.
Akkordeon
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Leader Tatiana Borodina
tatiana.borodina@mdc-berlin.de
Phone: 030 9406-1341
PublicationsWe operate an impressive line of sequencing platforms (Illumina, PacBio, Oxford Nanopore), pipetting robots and analytical equipment. 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 500, NovaSeq 6000;
- Long-read sequencing on Pacific Biosciences Sequel II;
- Long-read sequencing on Oxford Nanopore MinION and PromethION platforms
For consulting and assistance in planning of a sequencing experiment please contact us at seqteam@mdc-berlin.de or seqteam@bih-charite.de.
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 seqteam@mdc-berlin.de or to seqteam@bih-charite.de 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.
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Leader Thomas Conrad
thomas.conrad@mdc-berlin.de
Phone: 030 9406-1481The Single-cell Technologies unit provides access to an exceptionally wide range of cutting-edge single-cell multiomics approaches. 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
- FACS
- Droplet-based approaches (10X Genomics; Dolomite)
- Plate-based assays (Smart-Seq2/3; G&T-Seq; scBS+T-Seq)
- Spatial transcriptomics (10X Genomics Visium)
Single-cell Multiomics
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 FACS 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). FACS instruments can be booked under Provider Flow Cytometry Genomics, Mitte.
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Implementing a smooth and efficient NGS data flow from sequencers to users in a secure way is a more difficult task than one would expect, e.g. does NGS data processing, transfer and analysis still lack appropriate compression and standardization. Our group strives to optimize these tasks in a transparent and user-friendly way, using automated and reproducible software solutions for genomic data processing and analysis together with effective introduction of quality control measures.
For inquiries regarding genomics data management, please contact genomics data management via helpdesk-genomics@charite.de.
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Bastian Salewsky
bastian.salewsky@bih-charite.de
+49 30 450 669 048
Charité lab
Nucleic acids isolation | NGS library preparation | Illumina sequencingCarola Dietrich
carola.dietrich@mdc-berlin.de
MDC lab
Droplet- and plate-based single-cell genomicsCaroline Braeuning
caroline.braeuning@mdc-berlin.de
+49 30 9406-3043
MDC lab
FACS unit manager | Droplet-based single-cell genomicsCatrin Janetzki
catrin.janetzki@bih-charite.de
+49 30 450 569 048
Charité lab
NGS library preparation | Illumina sequencingClaudia Quedenau
quedenau@mdc-berlin.de
+49 30 9406-3048
MDC lab
Lab management (MDC lab) | PacBio and Oxford Nanopore sequencing coordination | NGS library preparationCornelia Schlee
cornelia.schlee@bih-charite.de
+49 30 450 669 048
Charité lab
NGS library preparation | Illumina sequencingCornelius Fischer
cornelius.fischer@mdc-berlin.de
+49 30 9406-1357
Data management | BioinformaticsDaniele Sunaga-Franze
daniele.franze@mdc-berlin.de
+49 30 9406-2995
LIMS Project managementElisabeth Kirst
elisabeth.kirst@charite.de
+49 30 9406-2995
MDC lab
NGS library preparation | Illumina sequencingFrancesca Solinas
Francesca.Solinas@mdc-berlin.de
+49 30 9406-1320
MDC lab
Droplet- and plate-based single-cell genomicsIzabela Plumbom
izabela.plumbom@mdc-berlin.de
+49 30 9406-1320
MDC lab
Droplet- and plate-based single-cell genomics | Spatial transcriptomicsJanine Altmüller
janine.altmueller@mdc-berlin.de
janine.altmueller@bih-charite.de
+49 30 9406-1434
Head of BIH/MDC Genomics Technology PlatformJeannine Wilde
jeannine.wilde@mdc-berlin.de
+49 30 9406-1321
MDC lab
Illumina sequencing coordination (MDC lab) | NGS library preparationKerim Secener
aliKerim.secener@mdc-berlin.de
+49 30 9406-1320
MDC lab
PhD studentKirsten Richter
kirsten.richter@mdc-berlin.de
Invoicing | Administrative support | Documentation management | Event organisationLorena Derezanin
lorena.derezanin@bih-charite.de
+49 30 450 569 048
Data management | BioinformaticsMadlen Sohn
madlen.sohn@mdc-berlin.de
+49 30 9406-3266
MDC lab
NGS library preparation | Illumina sequencingMarine Gil
marine.gil@charite.de
+49 30 9406-1342
MDC lab
Droplet-based single-cell genomicsMarko Vukovic
Marko.vukovic@mdc-berlin.de
MDC lab
Student assistantMarten Jäger
marten.jaeger@bih-charite.de
+49 30 450 569 048
Data management | BioinformaticsMichaela Seeger-Zografakis
mseeger@mdc-berlin.de
+49 30 9406-1324
MDC lab
FACS support | Droplet-based single-cell genomicsSarah Vitcetz
sarah.vitcetz@mdc-berlin.de
+49 30 9406-3041
MDC lab
Droplet- and plate-based single-cell genomics | Spatial transcriptomicsSomesh Sai
somesh.sai@mdc-berlin.de
+49 30 9406-1342
MDC lab
PhD studentTatiana Borodina
tatiana.borodina@mdc-berlin.de
+49 30 9406-1341
Team leader Next Generation SequencingThomas Conrad
thomas.conrad@mdc-berlin.de
+49 30 9406-1481
Team leader Single Cell TechnologiesUlrike Krüger
ulrike.krueger@bih-charite.de
+49 30 450 643 507
Charité lab
Project coordination and Lab management (Charité lab) | NGS library preparation | Illumina sequencingUte Ungethüm
ute.ungethuem@bih-charite.de
+49 30 450 676 272
Charité lab
Coordination of large-scale projects (Charité lab) | Automation of nucleid acid extraction and QC assays -
BIH
Christian Conrad
Stefanie Großwendt
Ute SchollMDC
Yo Lee
Ilaria Piazza
Nikolaus RajewskyGuests
Nils Blüthgen (Charité)
Anton Henssen (MDC/Charité)