GenomicsPlatform_Illumina_NovaSeq_FlowCells

Genomics

Janine Altmüller

Profil

The main focus of the Scientific Genomics Platforms lies on functional genome research using sophisticated next generation sequencing methodologies as well as a variety of single cell applications.

The facility is located at the Berlin Institute for Medical System Biology in Mitte, Berlin, and comprise of two separate units; Next Generation Sequencing and Single Cell Technologies.  

Next Generation Sequencing Unit (Dr. Tatiana Borodina)

The NGS Unit operates an impressive equipment park for sequencing and library preparation. We process more than 300 small- and large-scale service projects a year, for a diverse range of applications. The group has a profound experience in NGS-related technology development, implementation of novel protocols and library preparation automation.  

Available services and technologies include:

  • Consultations on NGS-related questions;
  • Support in experimental design of NGS projects;
  • QC for DNA and RNA samples and sequencing libraries;
  • Library preparation from bulk material for diverse -Seq applications (RNA, WGS, WES, ChiP, etc.) for Illumina, PacBio and Oxford Nanopore sequencing technologies;
  • Short-read sequencing on Illumina instruments: iSeq, MiniSeq, NextSeq 500, HiSeq 4000, NovaSeq 6000 instruments;
  • Long-read sequencing on Pacific Biosciences Sequel machine;
  • Long-read sequencing on Oxford Nanopore MinION and PromethION platforms.
  • Primary data processing & QC

 

Single-Cell Technologies Unit (Dr. Thomas Conrad)

The Single Cell Technologies unit provides access to an exceptionally wide range of cutting-edge single cell multi-omics 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; G&T-Seq; scBS+T-Seq)
  • Nanowell-based assays (Takara ICell8)
  • Spatial transcriptomics (10X Genomics Visium)
  • Primary data processing & QC
  • Bioinformatics support (for in-depth analyses, please also contact the BIH and MDC bioinformatics platforms)

 

Team

The Genomics Unit comprises of two teams; the Next Generation Sequencing Core Facility and the Single Cell Technologies unit, under the management of Tatiana Borodina and Thomas Conrad, respectively.

Next Generation Sequencing Core Facility 

Facility Manager

 

Scientists
 
Technical Assistants 

 

Single Cell Technologies Unit

Facility Manager
 
Scientists
 
Research Assistant 
 
Students

 

FACS Facility 

Publications

Next Generation Sequencing

Our services cover all stages of NGS projects, including experimental design, samples QC, library preparation, sequencing and data analysis.

For consulting and assistance in planning of the sequencing experiment please contact Dr. Tatiana Borodina - tatiana.borodina@mdc-berlin.de

NGS Services Prices

NB! Here is the NGS services pricelist valid for MDC and Charite users. Please contact us for the full cost calculation of your project.

Genomics Platform NGS Services Pricelist


Ordering

Services are currently ordered per email to seqteam@mdc-berlin.de or to the members of the Genomics Platforms – NGS Team you are already in contact with.

Following documents have to be filled and submitted to the Genomics Platforms:

1. Project registration form

Project Registration Form - Illumina NGS service

Project Registration Form - PacBio NGS service

Project Registration Form - Oxford Nanopore NGS service

This is a sequencing service agreement – it contains contact and billing information and detailed service description. Please follow instructions on the first page of the form to get it approved by the NGS team and your group leader.

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

2. DNA or RNA samples or sequencing libraries transfer sheet

for Illumina NGS service (select depending on the type of submitted samples):

Sequencing libraries transfer sheet - Illumina NGS service

DNA samples libraries transfer sheet - Illumina NGS service

RNA samples libraries transfer sheet - Illumina NGS service

for PacBio NGS service:
Samples Transfer Sheet - PacBio NGS service

for Oxford Nanopore NGS service:
Samples Transfer Sheet - Oxford Nanopore service

Enter information about your samples. For ready sequencing libraries a user-specific code has to be used to label tubes submitted to the Genomics Platform – NGS Unit; instructions and example are in the form 2a.

3. (if available) Sizes distribution profiles of submitted samples or seq. libraries

If you have no access to a BioAnalyser/TapeStation, this QC step can be also performed by the Genomics Platforms.

4. Requirements for submission of samples (RNA/DNA) and sequencing libraries

Nucleic acid samples guidelines 

Sequencing libraries requirements
 
Turnaround time

Generally, the projects are processed in the order of 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 sequencing libraries occupy the whole flowcell, usually they can be sequenced within 1-2 weeks after the samples 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 Technologies

Cell-to-cell variation detected by single-cell measurements can reveal deeper insights into the interplay of gene regulatory circuits and allows to determine the degree of biological plasticity and flexibility to react to environmental changes. Eventually, single-cell analysis approaches provide a unique opportunity to discover exclusive characteristics of a diseased cell state. 

The Single Cell Technologies Unit seeks to be at the forefront of the single cell multi-omics field with the aim to offer expertise assistance in all stages of the process from project – and experiment planning and design, sample preparation and data processing. 
As the world of single cell technologies has been rapidly evolving, we have over the years implemented novel approaches side by side with more streamlined methods in single cell research in order to be able to provide a service of high quality in the context of collaborative research projects.  
 

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[SNV1]  for further consultation.

Single Cell service prices will vary depending on the method of choice as well as project details such as sample numbers, etc. Once the details have been discussed with us, a quote for our services will be provided before we move forward with the planning.

After this, the project will be set up and managed via Open Iris, giving clients the possibility of following the process of their project along side with personal communication between the parties involved.

Janine Altmüller
Head
Dr. med. Janine Altmüller
Secretariat
Sabrina Deter
(030) 9406 2920

Genomics Platform on the BIH website