Open Lab for single cell sequencing (scOpenLab)

Overview

Single cell sequencing (sc-seq) technologies are evolving fast and become more and more important for many research groups at the DKFZ. To address this need, the DKFZ founded the single cell open lab (scOpenLab, cost center W192), which started operation in January 2018, with the generous support by DKFZ-HIPO (https://www.dkfz.de/en/hipo/) providing funding for the scOpenLab staff. The lab is headed by Jan-Philipp Mallm (j.mallm@dkfz.de) and is located in the Bioquant in room 423 on the 4th floor. The scOpenLab offers assisted access to instrumentation for processing the cells and preparing the libraries for sequencing to all DKFZ groups. To do these experiments successfully there will be regular training sessions. After having received training the systems can be booked at the scOpenLab. The sequencing libraries prepared in the scOpen Lab need to be submitted to the High Throughput Sequencing Unit of the DKFZ Genomics and Proteiomics Core Facility for sequencing. While the staff costs are covered by DKFZ-HIPO, the consumables for the experiments have to be bought by the individual users.

Available sc-seq readouts

Currently, the following workflows are available:

10x Genomics Chromium system (www.10xgenomics.com)

  • scRNA-seq (3' / 5' counting)
  • scVDJ-seq (+scRNA-seq)
  • scCNV-seq
  • CITE-seq (in evaluation)

Fluidigm C1 system (www.fluidigm.com)

  • scRNA-seq (full length / 3' counting)
  • scATAC-seq (high / low throughput)

InDrop (www.1cell-bio.com)

  • scRNA-seq (3' counting)

On plates

  • scRNA-seq (full length)
  • scATAC-seq (in evaluation)
  • G&T-seq

The portfolio of techniques and machines will be constantly updated and expanded in close interactions with the DKFZ groups of the sc-seq@dkfz network. Upcoming protocols will include scWGBS & multiomics read-outs. For all our protocols we aim for automation, miniaturization and compatiblity with frozen (cancer) tissue. 

Training and additional information

For all new users we offer an introduction into single-cell sequencing covering the different techniques, pros & cons, project design and lab logistics. The introduction is mandatory for all scOpenLab users who will then be able to book systems online (starting October 2018). Users will the be trained on a indivudual basis for each machine / technique in the lab according to their project.

The following dates are still available for the introduction:

  • 23.11.2018   9-11 am Bioquant, ground floor, Seminar room 044
  • 14.12.2018   9-11 am Bioquant, ground floor, Seminar room 044
  • 18.01.2019   9-11 am Bioquant, ground floor, Seminar room 044

If you would like to participate, please send an e-mail to: scopenlab@dkfz.de

 

Machines can be booked online, please create an account here: https://dkfzppms.inet.dkfz-heidelberg.de/scopenlab/

Please note that you can access our booking system only via the DKFZ network / VPN. 

Staff members

Dr. Jan-Philipp Mallm

Dr. Michelle Liberio

Katharina Bauer

Laura Giese

Contact

scOpen Lab (W192)
Bioquant Center, room 423
Im Neuenheimer Feld 267
69120 Heidelberg
Germany
Tel.: +49-6221-54-51321 (lab)
Tel.: +49-6221-54-51322 (office)
e-mail: scOpenLab@dkfz.de

 

 

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