GenomicsPlatform_Illumina_NovaSeq_FlowCells

Genomics

Janine Altmüller

Profil

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.

The facility comprises three teams: Next Generation Sequencing, Single-Cell Technologies 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. 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

 

Single-Cell Technologies Team (Dr. Thomas Conrad)

The Single-cell technologies team 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)

 

Data Management Team (Dr. Tomasz Zemojtel)

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)

Team

The BIH/MDC Genomics Technology Platform, headed by Janine Altmüller, comprises three teams: Next Generation Sequencing, Single-Cell Technologies and Data Management, under the management of Tatiana Borodina, Thomas Conrad and Tomasz Zemojtel, respectively.

Bastian Salewsky
bastian.salewsky@bih-charite.de
+49 30 450 669 048
Charité lab
Nucleic acids isolation | NGS library preparation | Illumina sequencing 

Carola Dietrich
carola.dietrich@mdc-berlin.de
+49 30 9406-3266
MDC lab
NGS library preparation | Illumina sequencing 

Caroline Brauening
caroline.braeuning@mdc-berlin.de
+49 30 9406-3043
MDC lab
FACS unit manager | Droplet-based single-cell genomics

Catrin Janetzki
catrin.janetzki@bih-charite.de
+49 30 450 569 048
Charité lab
NGS library preparation | Illumina sequencing 

Claudia Quedenau
quedenau@mdc-berlin.de
+49 30 9406-3048
MDC lab
Lab management (MDC lab) | PacBio and Oxford Nanopore sequencing coordination | NGS library preparation

Cornelia Schlee
cornelia.schlee@bih-charite.de
+49 30 450 669 048
Charité lab
NGS library preparation | Illumina sequencing 

Cornelius Fischer
cornelius.fischer@mdc-berlin.de
+49 30 9406-1357
Data management | Bioinformatics

Daniele Sunaga-Franze
daniele.franze@mdc-berlin.de
+49 30 9406-2995
LIMS Project management

Izabela Plumbom
izabela.plumbom@mdc-berlin.de
+49 30 9406-1320
MDC lab
Masters Student

Janine Altmüller
janine.altmueller@mdc-berlin.de 
janine.altmueller@bih-charite.de
+49 30 9406-1434
Head of BIH/MDC Genomics Tehnology Platform

Jeannine Wilde
jeannine.wilde@mdc-berlin.de
+49 30 9406-1321
MDC lab
Illumina sequencing coordination (MDC lab) | NGS library preparation

Kerim Secener
aliKerim.secener@mdc-berlin.de
+49 30 9406-1320
MDC lab
PhD student

Kirsten Richter
kirsten.richter@mdc-berlin.de
Invoicing | Administrative support | Documentation management | Event organisation

Madlen Sohn
madlen.sohn@mdc-berlin.de
MDC lab
NGS library preparation | Illumina sequencing 

Marine Gil
marine.gil@charite.de
+49 30 94061342
MDC lab
Droplet-based single-cell genomics

Marten Jäger
marten.jaeger@bih-charite.de
+49 30 450 569 048
Data management | Bioinformatics

Michaela Seeger-Zografakis
mseeger@mdc-berlin.de
+49 30 9406-1324
MDC lab
FACS support | Droplet-based single-cell genomics

Sarah Vitcetz
sarah.vitcetz@mdc-berlin.de
+49 30 9406-3041
MDC lab
Droplet- and plate-based single-cell genomics | Spatial transcriptomics

Somesh Sai
somesh.sai@mdc-berlin.de
+49 30 9406-1342
MDC lab
PhD student

Tatiana Borodina
tatiana.borodina@mdc-berlin.de
+49 30 9406-1341
Team leader Next Generation Sequencing

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

Tomasz Zemojtel
tomasz.zemojtel@bih-charite.de
+49 30 450 643 527
Team leader Data Management

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

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

Publications

Next Generation Sequencing

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

For consulting and assistance in planning of a sequencing experiment please contact us at seqteam@mdc-berlin.de or seqteam@bih-charite.de.

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.

Single-Cell Technologies

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, interactions, and developmental trajectories.

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.

Dr. med. Janine Altmüller
Head
Dr. med. Janine Altmüller