Genomics Technology platform

The facility comprises four teams: Next Generation Sequencing, Single-Cell Technologies, Flow Cytometry and Data Management. 

Next Generation Sequencing Team (Dr. Tatiana Borodina)

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

Single-Cell Technologies Team (Dr. Thomas Conrad)

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)

Flow Cytometry Team (Caroline Braeuning)

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 and booking at FacsBimsb@mdc-berlin.de .

Data Management Team (Dr. Marten Jäger)

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.

Steering Committee

BIH
Christian Conrad
Stefanie Großwendt
Ute Scholl

MDC
Yo Lee
Ilaria Piazza
Nikolaus Rajewsky

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

NGS Services Prices

Actual pricelist valid for MDC and Charité users is available upon request.

Large-scale projects require individual cost calculation - please contact seqteam@mdc-berlin.de or seqteam@bih-charite.de.

Ordering

Services are currently ordered per email to seqteam@mdc-berlin.de or to seqteam@bih-charite.de  or to the members of the NGS team 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.

Turnaround time

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 your ready 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.