Single-Cell Open Lab (scOpen Lab)

Single cell sequencing (sc-seq) technologies are evolving fast and become more and more important for many research groups. To address this need, the DKFZ single cell open lab (scOpen Lab, DKFZ W192) started work in January 2018. Funding for the scOpenLab staff is generously provided by DKFZ-HIPO (

The lab is headed by Jan-Philipp Mallm ( and is located in the Bioquant in room 423 on the 4th floor. The scOpen Lab 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 the training systems can be booked at the scOpen Lab.


Currently, workflows for 3’-UMI single-cell RNA seq and T-cell receptor profiling with the 10x Genomics Chromium system ( as well as scRNA-seq on the Fluidigm C1 system ( are available. The portfolio of techniques and machines will be constantly updated and expanded in close interactions with the sc-seq community at the DKFZ. While the staff costs are covered by DKFZ-HIPO, the consumables for the experiments have to be bought by the individual users. Usage of the 10x Genomics system for University of Heidelberg researchers is via David Ibberson at the Cellnetworks Deep Sequencing Core Facility and for the EMBL via their Genomics Core Facility.

Training schedule

The first training session for scRNA-seq on the Chromium drop-seq system will take place on 24th January 2018. If you are interested to participate, please send an email to

Additional information and protocols


Philipp Mallm

scOpen Lab (BQ24)

Im Neuenheimer Feld 267

69120 Heidelberg


BioQuant room 423

Tel.: +49-6221-54-51321
e-mail: scopenlab (at)