Core facilitiesDeep Sequencing Lab

The CellNetworks Deep Sequencing Core Facility was opened in September 2010 to provide access to Next Generation Sequencing technology (NGS), for the Heidelberg University research community. The Core Facility is supported by the Excellence Cluster CellNetworks, the Centre for Organismal Studies (COS Heidelberg), Heidelberg Molecular Life Sciences (HMLS) Research Council and the Excellence Strategy Field of Focus 1.

The facility was founded with the intent to not only provide library preparation and sequencing for its users on campus, but also to offer professional advice on how to implement NGS into research. This advice has been widely taken up and has in some cases led to the development of new protocols or the refinement of current “standard” protocols. In addition, it is widely recommended that users speak with us before initiating a project, in order to clear up any mis-conceptions about NGS, which will inevitably save money and time.

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With regards to services, the Core Facility offers a mixture of services for its users. The main day to day activities revolve around the standard library preparation methods for Illumina sequencing. However, due to the high diversity in sample genome origin on campus, and the fact that reagents are tailored to samples originating from humans and mice, the library preparations are often tailored to the individual needs.

“Standard” library preparations on offer:

  • RNA-Seq (as of June 2014 all libraries are strand specific)
  • Small RNAseq
  • Chip-Seq
  • gDNA-Seq (de novo, resequencing)
  • Target Enrichment
  • Single Cell Sequencing
  • Single Cell on 10x Chromium Platform

Instrumentation:

The Core Facility has in the previous years maintained a successful collaboration with the Genomics Core Facility of EMBL. We have access to the following sequencing instruments:

  1. NextSeq 550 - A desktop based sequencer with quick turnaround time and high sequencing adaptability
  2. HiSeq 4000 - Large scale/production scale sequencer
  3. MiSeq - Desktop sequencer with low output, ideal for testing of new protocols or amplicon libraries.

In addition, we have the following instruments to help with library preparation:

  1. Covaris S2 sonicator
  2. Bioanalyzer - capillary electrophoresis instrument which aids to analyze RNA quality and view the library products prior to sequencing.
  3. 10x Chromium System - single cell capture system for transcription profiling and ATACseq.