Home | Facilities | NGS and Data Technologies NGS and Data Technologies Mission The Next Generation Sequencing (NGS) Core Facility’s mission is to provide the local research community with access to state-of-the-art sequencing technologies, and to help facilitate cutting-edge omics research. We offer consultation and expert assistance in strategic planning and method development, library preparation, and high-throughput sequencing services for bulk and single-cell applications. We also support in data processing, management, and analysis. About Prof. Rehli About the NGS Core Services We are an academic sequencing core unit and offer a broad spectrum of NGS methodologies. Our services include consultation on experimental design, library preparation for various applications, sequencing, bioinformatics training and support, and computational analyses (primary, secondary, and tertiary). We also work in close collaboration with the University of Regensburg and the University Hospital Regensburg to further enhance the capabilities of sequencing technologies. Consultation If you are preparing a grant application and/or plan to perform NGS experiments, please be sure to discuss your experimental setup with us in advance. We take the time to discuss possible applications and experimental designs to ensure the best possible outcome for your projects and grant applications. Please make an appointment with ngs-core@lit.eu and fill out the Consultation Form. NGS Services and Applications We offer a broad range of NGS applications for bulk and single cells (droplet-based, 10X Genomics), including sample preparation, QC and library preparation. For standard applications and collaborative projects, please see our current list of services and prices. If the service you need is not listed, please contact ngs-core@lit.eu. Training We offer introductory courses to bioinformatics, enabling students and researchers to conduct large parts of their analyses themselves and to present their data plots at publication-grade standard. Bioinformatics for PhD students I – please register here: https://elearning.uni-regensburg.de/course/view.php?id=57074 Bioinformatics for PhD students in R – please register here: https://elearning.uni-regensburg.de/course/view.php?id=58464 Bioinformatics Support We provide three levels of bioinformatics services: Primary data processing: demultiplexing, mapping to a reference genome and quality control for all commonly used techniques. For specific applications, please inquire: ngs-core@lit.eu Secondary analysis by in-house analysis pipelines: including principal component analysis, calling of differentially expressed genes, pathway analysis and clustering, if applicable. Custom analysis and visualization depending on available resources. Data Management Modern high-throughput technologies produce large amounts of data that come with experimental, instrument and additional metadata. Complete and standardized metadata enables us to develop software solutions for automated processing and data analysis, as well as access and encryption management. This high degree of automation ensures efficiency and reproducibility. In addition, we also provide support on data management topics in general and specifically data management plans (DMPs) upon request. If you have questions related to data management, please contact ngs-core@lit.eu. User Information Our NGS Core Facility offers a range of paid services that include plain sequencing on our short-read sequencer, NextSeq 2000. We also offer library preparation services, including sample preparation and quality controls (QC) for collaborative projects. Click here to review our terms and conditions: “Operational Protocol.” Collaborative sequencing projects Please note the following protocol: Consultation is required before any collaborative sequencing project to discuss both the technical and organizational details of your project. Please make an appointment with ngs-core@lit.eu and fill out our Consultation Form. After this consultation, the collaborating partner will receive a quotation outlining costs. Please note that the expenses for sample preparation, library preparation, and sequencing must be covered by the institution or the Principal Investigator requesting our services. Communication channels will be established between participating parties. All technical processing will be done in close collaboration with the collaboration partner/user. Using the NGS service (sequencing only) Please note the following protocol: The sequencing service is limited to research use only. We will not consider other applications. A user can request the sequencing service by completing our Booking Request and returning it to ngs-core@lit.eu. That user will then receive a cost quotation. Note that expenses for flow cells, library pooling & QC (if applicable), and service fees must be covered by the institution or the Principal Investigator requesting the service. External users may wish to bring their own flow cells. Users should transfer samples to the NGS Core and provide a sample sheet for subsequent demultiplexing. Users will be notified once sequencing has been performed, and will receive a link to download the data. If the sequencing data is published, the author must acknowledge the services provided by the NGS Core. Selection of the most important publications from the last few years: Dittmar DJ, Pielmeier F, Strieder N, Fischer A, Herbst M, Stanewsky H, Wenzl N, Roseler E, Eder R, Gebhard C, Schwarzfischer-Pfeilschifter L, Albrecht C, Herr W, Edinger M, Hoffmann P, Rehli M. Donor regulatory T cells rapidly adapt to recipient tissues to control murine acute graft-versus-host disease. Nat Commun. 2024 Apr 15. 15:3224. doi:10.1038/s41467-024-47575-z. PMID:38622133 Delacher M, Schmidleithner L, Simon M, Stuve P, Sanderink L, Hotz-Wagenblatt A, Wuttke M, Schambeck K, Ruhland B, Hofmann V, Bittner S, Ritter U, Pant A, Helbich SS, Voss M, Lemmermann NA, Bessiri-Schake L, Bohn T, Eigenberger A, Menevse AN, Gebhard C, Strieder N, Abken H, Rehli M, Huehn J et al. The effector program of human CD8 T cells supports tissue remodeling. J Exp Med. 2024 Feb 5. 221doi:10.1084/jem.20230488. PMID:38226976 Schwartz U, Komatsu T, Huber C, Lagadec F, Baumgartl C, Silberhorn E, Nuetzel M, Rayne F, Basyuk E, Bertrand E, Rehli M, Wodrich H, Laengst G. Changes in adenoviral chromatin organization precede early gene activation upon infection. EMBO J. 2023 Aug 29.e114162. doi:10.15252/embj.2023114162. PMID:37641864 Sorrentino A, Menevse AN, Michels T, Volpin V, Durst FC, Sax J, Xydia M, Hussein A, Stamova S, Spoerl S, Heuschneider N, Muehlbauer J, Jeltsch KM, Rathinasamy A, Werner-Klein M, Breinig M, Mikietyn D, Kohler C, Poschke I, Purr S, Reidell O, Martins Freire C, Offringa R, Gebhard C, Spang R et al. Salt-inducible kinase 3 protects tumor cells from cytotoxic T-cell attack by promoting TNF-induced NF-kappaB activation. J Immunother Cancer. 2022 May. 10doi:10.1136/jitc-2021-004258. PMID:35606086 Delacher M, Simon M, Sanderink L, Hotz-Wagenblatt A, Wuttke M, Schambeck K, Schmidleithner L, Bittner S, Pant A, Ritter U, Hehlgans T, Riegel D, Schneider V, Groeber-Becker FK, Eigenberger A, Gebhard C, Strieder N, Fischer A, Rehli M, Hoffmann P, Edinger M, Strowig T, Huehn J, Schmidl C, Werner JM et al. Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells. Immunity. 2021 Apr 13. 54:702-720 e717. doi:10.1016/j.immuni.2021.03.007. PMID:33789089 Kappelmann-Fenzl M, Gebhard C, Matthies AO, Kuphal S, Rehli M, Bosserhoff AK. C-Jun drives melanoma progression in PTEN wild type melanoma cells. Cell Death Dis. 2019 Aug 5. 10:584. doi:10.1038/s41419-019-1821-9. PMID:31378787 Vatter S, Schmid M, Gebhard C, Mirbeth C, Klobuch S, Rehli M, Herr W, Thomas S. In-vitro blockade of the CD4 receptor co-signal in antigen-specific T-cell stimulation cultures induces the outgrowth of potent CD4 independent T-cell effectors. J Immunol Methods. 2018 Mar. 454:80-85. doi:10.1016/j.jim.2017.11.006. PMID:29154771 Equipment NextSeq 2000 The NextSeq 2000 is Illumina’s most flexible benchtop sequencing system. It offers several flow-cell types generating output from 100 to 1200 million reads per sequencing direction, with a read length of up to 2 x 300 basepairs (bp). This short-read sequencer is appropriate for most small to intermediate-sized sequencing projects. Large projects can be sequenced externally to ensure cost efficiency. Additional equipment For the preparation of sequencing libraries and quality control, the following devices are available at the NGS Core: Tapestation 2200/4150 (Agilent Technologies)–DNA/RNA quality control Qubit 2.0 Fluorometer (Thermo Fisher Scientific)–Quantification of DNA/RNA Nanodrop (ND-1000)–Quantification of DNA/RNA S220 sonicator (Covaris)–fragmentation of DNA SONIFIER 250 (Branson)–fragmentation of DNA Chromium iX (10X Genomics)–single cell or nuclei based protocols Team NGS Core Team Core team Prof. Michael Rehli Head of NGS Core Dr. Claudia Gebhard Senior Scientist Dr. Nicholas Strieder Senior Scientist Dr. Jakob Simeth Postdoctoral Scientist Dr. Inmaculada Hernandez-Lopez Postdoctoral Scientist Fabian Hoelzl PhD Student Johanna Raithel Research Technician Dr. Alexander Fischer Postdoctoral Scientist Previous Next Close Dr. Claudia Gebhard Senior Scientist NGS and Data Technologies Tel: +49 941 944-18186 Email: Claudia.Gebhard@ukr.de Close Dr. Nicholas Strieder Senior Scientist NGS and Data Technologies Tel: +49 941 943-68551 Email: Nicholas.Strieder@ukr.de Nicholas Strieder studied Biology at the University of Regensburg, focusing on cell biology. During a one year Erasmus exchange at the University of Leicester he was involved in protein import into chloroplasts and protein structure analysis using crystallography and nuclear magnetic resonance spectroscopy techniques. Following his graduation in yeast protein biology, he performed his PhD in the lab of Prof. G. Meister on miRNA mediated regulation in human cells applying high-throughput sequencing methods. In 2014 he joined the Statistical Bioinformatics Lab of Prof. R. Spang focusing on bioinformatic analysis of NGS data sets. After a 3 year postdoc phase he went to industry and worked on the bioinformatic analysis of food contaminating bacteria with long and short read sequencing methods at Labor Kneißler Burglengenfeld. In 2019 he joined the LIT and contributed by establishing the Bioinformatics Unit of the NGS-Core. Dr. Nicholas Strieder works on the bioinformatic analysis of bulk and single cell high-throughput sequencing data with a focus on T cell development and function in heathy tissue and disease in collaboration with the research groups of the LIT. Close Dr. Jakob Simeth Postdoctoral Scientist NGS and Data Technologies Tel: +49 941 943-68553 Email: Jakob.Simeth@ukr.de Jakob Simeth studied Computational Science and Physics in Regensburg. During his PhD in particle physics simulations, he was co-responsible for data sharing and archiving in a large, trans-European collaboration, where he gained experience in automatic data processing and data management in general. Later, when working in the group of Rainer Spang, he focused on bioinformatic algorithms and further pursued projects in data annotation and provenance tracking. In the NGS Core at the LIT, Jakob Simeth is responsible for research data management. Building on a broad knowledge in IT, he continues to work on the automation of data management processes, improving the efficiency and user experience for all members and users of the core. His mission is to make data produced at the LIT as openly accessible and findable (FAIR) as possible while ensuring the necessary security levels and safety measures for human genetic data. Close Dr. Inmaculada Hernandez-Lopez Postdoctoral Scientist NGS and Data Technologies Tel: +49 941 943-68550 Email: Inmaculada.Hernandez-Lopez@ukr.de Inmaculada Hernández López studied Biotechnology at the Polytechnic University of Valencia, Spain. Starting in 2012, she did a PhD in the field of Biotechnology and Bioinformatics at BOKU University in Vienna, Austria, under the supervision of Prof. Nicole Borth. Together they have worked on the transcriptomic and epigenomic characterization of Chinese Hamster Ovary (CHO) cells. During her PhD, she pioneered the epigenomic analysis of CHO cells in Prof. Borth’s group, both experimentally and computationally: producing, analyzing and publishing the first reference epigenomes for CHO cells at different culture conditions. Furthermore, she did a 9 months placement on the statistical genomics group from CNAG-CRG Barcelona. Concurrently, she completed a post-graduate Masters degree in bioinformatics and biostatistics at the University of Barcelona. In a further position at the Institute of Cellular Medicine, Newcastle University (UK), starting in 2016, she developed new analytical strategies to integrate gene expression, epigenomic and 3D genome organization data from men and women in immune cells. Furthermore, she provided help to undergraduate and PhD students to improve their bioinformatic skills. During her last position, she was employed as a computational Marie Curie Postdoctoral Fellow at the Single Cell Genomics Team at the National Centre for Genomic Analysis (CNAG-CRG) in Barcelona. There, she focused on the systematic integration of genomic data from individual cells to characterize the underlying phenotype. She was working on several projects in collaboration with diverse hospitals in Spain and Germany, where they characterized the immune landscape and tumour tissues under the effect of different treatments in diseased individuals compared to healthy. In 2021, she joined the LIT as a bioinformatician in the Bioinformatics Unit of the NGS-Core. Close Fabian Hoelzl PhD Student NGS and Data Technologies Tel: +49 941 944-18188 Email: Fabian.Hoelzl@ukr.de Fabian Hölzl earned his Master’s degree in Biochemistry from the Technical University Munich. In 2022, he embarked on his doctoral journey under the guidance of Prof. Rehli, focusing on cohesin mutations in myeloid malignancies. His research delves into the intricate mechanisms of how the loss of cohesin disrupts the spatial and functional chromatin organization within cells. Close Johanna Raithel Research Technician NGS and Data Technologies Tel: +49 941 944-18189 Email: Johanna.Raithel@ukr.de Close Dr. Alexander Fischer Postdoctoral Scientist NGS and Data Technologies Tel: +49 941 943-38477 Email: Alexander.Fischer@ukr.de Contact For general inquiries Email: NGS-core@lit.eu For specific inquiries or to schedule an appointment Prof. Michael Rehli Head of Next Generation Sequencing (NGS) Core Tel: +49 941 944–38187 Office: D53.330 Visit Professor Rehli’s PI page here! Dr. Claudia Gebhard Wet-lab Unit Tel: +49 941 944–18186 Office D54.280 Dr. Nicholas Strieder Bioinformatics Unit Tel: +49 941 943–68551 Office V801 / Bajuwarenstr. 4 Dr. Jakob Simeth Data Management Unit +49 941 943–68553 Office V803 / Bajuwarenstr. 4 Address Leibniz Institute for Immunotherapy University Hospital of Regensburg Research building D5 Franz-Josef-Strauß-Allee 11 93053 Regensburg, Germany
