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Core Facility – DEEPSEQ Deep Sequencing Facility

The Deep Sequencing Core Facility was established in September 2010 to provide the Neuenheimer Feld Campus with access to Next Generation Sequencing (NGS). We provide the possibility to construct libraries for sequencing with the focus not only on the „standard“ application but on the establishment of custom protocols which can be of benefit to the entire campus.

Sequencing is available on a variety of instruments all based on the Illumina Sequencing by Synthesis technology, i.e. NGS Library Preparation or Single Cell Library Preparation for 10x Chromium NGS Sequencing. In addition to library preparation and sequencing we also help with planning sequencing experiments and offer advice on projects.

Project requests

All researchers from Heidelberg University and the Health + Life Science Alliance Heidelberg Mannheim are welcome to request help or place orders for Next Generation Sequencing analyses. Projects funded through company funding unfortunately cannot be accepted.

Deep Seq Timeline with the steps: First contact, research plan, online request, sample submission, lab work, anlalysis results

Before sample submission please:

follow the steps of our sample submission guide with specified requirements for different sample types (download document).
read carefully the iLabs sample registration guideline (download document)
see our end-user license agreement (EULA; download PDF) for more general information on the Deep Sequencing Core Facility's services as well as users' rights and duties. New customers are requested to bring a signed copy of the EULA when submitting the first sample set.

Sample registration

Services & Equipment

SERVICES

NGS Library Preparation (Illumina Platform)
- Bulk RNA library preparation (poly-A capture, rRNA and/or globin depletion, tagmentation)
- Small RNA library preparation
- ChIP-seq
- gDNA library preparation (de novo or resequencing)
- Target enrichment
Single-cell library preparation (10X Genomics and Parse Biosciences)
Spatial transcriptomics library preparation (10X Genomics Visium, Visium HD).
NGS Sequencing (Illumina Platform)

We accommodate, after discussion with staff, custom protocols brought by users.

EQUIPMENT

Illumina MiniSeq (22-25 million reads output)
Illumina NextSeq 2000 (100 million to 1.8 billion reads output)
In collaboration with EMBL: Pacbio and Oxford Nanopore (EMBL GeneCore)
10X Genomics Chromium X
10X Genomics CytAssist
Covaris S2 Sonicator
Agilent Bioanalyzer 2100

Team

Tabelle

	David Ibberson Head of Facility Deep Sequencing Lab BQ 40 BioQuant INF 267 69120 Heidelberg Office: +49 6221 54 51359 / Rm 001 Lab: +49 6221 54 51369 / Rm 606 / U27 david.ibberson@bioquant.uni-heidelberg.de
	Bianka Berki , PhD NGS and Spatial Omics Specialist bianka.berki@bioquant.uni-heidelberg.de
Group contact email:	deepseqlab@bioquant.uni-heidelberg.de

Selected publications

Tabelle

Zhang, Y., Jiang, Y., Kuster, D., Ye, Q., Huang, W., Fürbacher, S., Zhang, J., Doll, P., Lin, W., Dong, S., Wang, H., Tang, Z., Ibberson, D., Wild, K., Sinning, I., Hyman, A.A., Jäschke, A., 2025. Single-step discovery of high-affinity RNA ligands by UltraSelex. Nat. Chem. Biol. 21, 1118–1126.
Zaremba, B., Fallahshahroudi, A., Schneider, C., Schmidt, J., Sarropoulos, I., Leushkin, E., Berki, B., Poucke, E.V., Jensen, P., Senovilla-Ganzo, R., Hervas-Sotomayor, F., Trost, N., Lamanna, F., Sepp, M., García-Moreno, F., Kaessmann, H., 2025. Developmental origins and evolution of pallial cell types and structures in birds. Science.
Meyer, M., Parpoulas, C., Barthélémy, T., Becker, J.P., Charoentong, P., Lyu, Y., Börsig, S., Bulbuc, N., Tessmer, C., Weinacht, L., Ibberson, D., Schmidt, P., Pipkorn, R., Eichmüller, S.B., Steinberger, P., Lindner, K., Poschke, I., Platten, M., Fröhling, S., Riemer, A.B., Hassel, J.C., Roberti, M.P., Jäger, D., Zörnig, I., Momburg, F., 2024. MediMer: a versatile do-it-yourself peptide-receptive MHC class I multimer platform for tumor neoantigen-specific T cell detection. Front. Immunol. 14.
Fallahshahroudi, A., Rodríguez-Montes, L., Taemeh, S.Y., Trost, N., Tellez, M., Ballantyne, M., Idoko-Akoh, A., Taylor, L., Sherman, A., Sorato, E., Johnsson, M., Moreira, M.C., McGrew, M.J., Kaessmann, H., 2024. A male-essential microRNA is key for avian sex chromosome dosage compensation. bioRxiv 2024.03.06.581755.
Laura Binmöller, Christopher Volkert, Christiane Kiefer, Luise Zühl, Magdalena W Slawinska, Anna Loreth, Berit H Nauerth, David Ibberson, Rafael Martinez, Terezie M Mandakova, Reinhard Zipper, Anja Schmidt. Differential expression and evolutionary diversification of RNA helicases in Boechera sexual and apomictic reproduction. J of Experimental Botany, Volume 75, Issue 8, 15 April 2024, Pages 2451–2469.
Liu, K., Wehling, L., Wan, S., Weiler, S.M.E., Tóth, M., Ibberson, D., Marhenke, S., Ali, A., Lam, M., Guo, T., Pinna, F., Pedrini, F., Damle-Vartak, A., Dropmann, A., Rose, F., Colucci, S., Cheng, W., Bissinger, M., Schmitt, J., Birner, P., Poth, T., Angel, P., Dooley, S., Muckenthaler, M.U., Longerich, T., Vogel, A., Heikenwälder, M., Schirmacher, P., Breuhahn, K., 2024. Dynamic YAP expression in the non-parenchymal liver cell compartment controls heterologous cell communication. Cell. Mol. Life Sci. 81, 115.
Yousuf, S., Qiu, M., Voith von Voithenberg, L., Hulkkonen, J., Macinkovic, I., Schulz, A.R., Hartmann, D., Mueller, F., Mijatovic, M., Ibberson, D., AlHalabi, K.T., Hetzer, J., Anders, S., Brüne, B., Mei, H.E., Imbusch, C.D., Brors, B., Heikenwälder, M., Gaida, M.M., Büchler, M.W., Weigert, A., Hackert, T., Roth, S., 2023. Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer. Gastroenterology 165, 891-908.e14.
Huth, T., Dreher, E., Lemke, S., Fritzsche, S., Sugiyanto, R., Castven, D., Ibberson, D., Sticht, C., Eiteneuer, E., Jauch, A., Pusch, S., Albrecht, T., Goeppert, B., Candia, J., Xin Wei Wang, Junfang Ji, Marquardt J. U., Nahnsen, S., Schirmacher, P. and Roessler S., 2023. C Chromosome 8p engineering reveals increased metastatic potential targetable by patient-specific synthetic lethality in liver cancer. Science Advances, 9,eadh1442(2023)

Funding Resources

4 Logos are displayed: Health &Lifescence alliance, Multispace platform, University of heidelberg, COS - Center for organismal studies

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