Genomics

The facility comprises three teams: Next Generation Sequencing, Single-Cell Technologies and Data Management. Please inform yourself about our terms and conditions if you plan to make use of our services.

Next Generation Sequencing Team (Dr. Tatiana Borodina)

We 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 2000, NovaSeq 6000, NovaSeq X plus;
• Long-read sequencing on Pacific Biosciences Sequel II;
• 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. 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 + Xenium; Nanostring GeoMx + CosMx)

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, the group 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.

Eventually, single-cell multi-omics 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. 

As all single-cell projects require individual organization and individual project planning and sample handling, please contact Dr. Thomas Conrad – Thomas.Conrad@mdc-berlin.de for further consultation.

Please contact Caroline Braeuning (Caroline.Braeuning@mdc-berlin.de) for access to FACS.