Leistungen
We will perform an integrative analysis based on merged data repository combining all datasets obtained
The ESPACE pipeline will be provided to HCA community
Integrative analysis of D3.1 and D.3.2 data, compared to those generated from healthy pancreata in WP2Data from isolated islets from the adultD and T2D groups will be compared to each other and compared to the healthy pancreas adult group
sNucRNA Seq data from isolated islets from the adultD and T2D groupssNucRNA Seq will be performed for ten ideally five male five female isolated islets from the T2D group and four ideally two male two female isolated islets from the agesex matched adultD group
Project WebsiteThe project website will form a central platform to showcase all aspects of the project including information on the consortium and its members the project objectives and workplan upcoming events and project publications Social media links will facilitate the widespread dissemination of information
Epigenomic map analysis of purified alpha, beta and delta cell populations from the adultD and T2D groupsWe will perform epigenomic profiling of isolated islets in bulk from adultD and T2D samples DNA methylation and histone modifications procured in WP1
The dissemination toolkit will be provided to all partners and will include a professional corporate identity including a project logo and styleguide dissemination and marketing materials such as project postcards or lanyards and templates for presentations reports meeting and internal documents
Protocol for IHC in freshly frozen and FFPE pancreas samplesTUM will provide the protocol for immunohistochemistry in freshly frozen and FFPE pancreas samples
Highly multiplexed imaging of 25 TMA using panels from D4.2 and D4.3We will perform highly multiplexed imaging of 25 TMA with about 25 TMA core samples per array summing up to a total of over 600 samples
First Industry working group meetingReport on the first meeting of the IT industry working group as established by STZ
Validated antibody panel for cell identity candidatesWe will generate a novel antibody panel containing markers for candidate proteins with variable expression in subtypes of the known pancreas cells and validate it for usage in freshly frozen and FFPE pancreas samplesWe will use the HPA resource to create novel validated antibody panels for subsequent high parametric analysis of protein expression in the pancreas using the CODEX technology The antibody panel will be generated and validated for usage in freshly frozen and FFPE pancreas samples and contain the following a markers for known cell types in pancreas D44 b candidate proteins with variable expression in subtypes of the known pancreas cells D45 c a proliferation marker and d markers for cellular organelles plasma membrane Golgi apparatus mitochondria nucleus to allow for cell segmentation and highdefinition phenotypic analysis
Provision of InfrastructureInfrastructure for data storage as well as data and cloud computing will be provided
Validated antibody panel for known cell types and proliferation markersWe will generate a novel antibody panel containing markers for known cell types in pancreas, and validate it for usage in freshly frozen and FFPE pancreas samples
Assessment of tissue morphologyTUM will control the pancreatic tissue for any impairment of the pancreas architecture and cellular composition inflammatory or neoplastic change
Social media reportThe social media report will summarize social media support centrally provided to the consortium as well as social media presence of the ESPACE project
Management SOPsAll relevant project management rules and regulations the final set of contractual documents project tasks and deliverables as well as an overview of all project internal workflows will be communicated to each partner and summarised in a booklet that will handed out at the kickoff meeting
Dockerised PipelinesAll single cell analysis pipelines will be developed following the HCA requirements ansd according to policies All pipelines will be provided via dockerized versions and being included into standardized analysis frameworks
Spatial analysis of cell identity candidate gene expression, cell types and cell type distributionWe will identify and analyse the cell types in the pancreas and their heterogeneity in terms of cell identity candidate gene expression combining image processing alignment deconvolution cell segmentation and quantification of all the markers included in the CODEX staining Based on a mixture of the tools of network theory and machine learning the spatial organization of both local and higher order cellular communities will be analysed
Standardisation of workflowsThe team from TUM will distribute their standardised protocols and workflows to the people at LUMC and OSR who will be responsible for tissue sampling there
Report on annual project meetingsThis deliverable will document annual project meetings including agenda participants decisions taken and initiated follow up activities
Training and workshopIn year 1 STZ will organise a workshop for the associated partners of ESPACE and further SMEs and companies that share the same interest in using the Human Cell Atlas of the Pancreas as reference map This workshop will present biological data the progress and the goals of the Human Cell Atlas of the Pancreas methodological improvements and efforts in the T2D part of the study A second workshop will be geared towards the health IT industries including European SMEs and global IT players and implemented in year 2 of the project
Second industry working group meetingReport on the second meeting of the IT industry working group as established by STZ
scRNA Seq from rare cell types from healthy pancreata from the adult group will be performed on an Illumina NovaSeq6000 sequencing system Libraries will be multiplexed and sequenced to an average depth of 50100000 reads per cell
scATAC Seq from healthy pancreata from adult and foetal groupsMultiregional scATAC Seq of ten ideally five male five female pancreas samples from healthy adult individuals and of eight ideally two of each two gestation weeks between week 1220 foetal pancreas samples from gestation week 12 to 20
sNucRNA Seq from healthy pancreata from adult and foetal groupssNucRNA Seq from healthy pancreata of ten ideally five male five female pancreas samples from adult individuals and of eight ideally two of each two gestation weeks between week 1220 foetal pancreas samples from gestation week 12 to 20
Pipelines in OTPAll single cell analysis pipelines will be included into our data processing framework One Touch Pipeline OTP
Protocol for the isolation of rare pancreas cell types using GateID for trainingProtocol for the isolation of rare pancreas cell types using GateID for trainingidentification of physical properties of rare cell types in the cell sorter which are then isolated for highthroughput transcriptome profiling
Knowledge sharing with/training of partner teams in LUMC and OSRTUM will share their knowledge with their partner teams in LUMC and OSR and provide necessary training to ensure standardised tissue sampling
The DMP will describe the data management life cycle for the data to be collected processed andor generated by ESPACE and will include information on the handling of research data during after the end of the project what data will be collected processed andor generated which methodology standards will be applied whether data will be sharedmade open access and how data will be curated preserved including after the end of the projectAny isses related to the protection of personal data will be dealt with in the respective ethics requirement POPD D71
Veröffentlichungen
Autoren:
Saskia Trump, Soeren Lukassen, Markus S. Anker, Robert Lorenz Chua, Johannes Liebig, Loreen Thürmann, Victor Max Corman, Marco Binder, Jennifer Loske, Christina Klasa, Teresa Krieger, Bianca P. Hennig, Marey Messingschlager, Fabian Pott, Julia Kazmierski, Sven Twardziok, Jan Philipp Albrecht, Jürgen Eils, Sara Hadzibegovic, Alessia Lena, Bettina Heidecker, Thore Bürgel, Jakob Steinfeldt, Christ
Veröffentlicht in:
Nature Biotechnology, Ausgabe 39/6, 2021, Seite(n) 705-716, ISSN 1087-0156
Herausgeber:
Nature Publishing Group
DOI:
10.1038/s41587-020-00796-1
Autoren:
Soeren Lukassen, Robert Lorenz Chua, Timo Trefzer, Nicolas C Kahn, Marc A Schneider, Thomas Muley, Hauke Winter, Michael Meister, Carmen Veith, Agnes W Boots, Bianca P Hennig, Michael Kreuter, Christian Conrad, Roland Eils
Veröffentlicht in:
The EMBO Journal, Ausgabe 39/10, 2020, ISSN 0261-4189
Herausgeber:
Nature Publishing Group
DOI:
10.15252/embj.20105114
Autoren:
Dana Avrahami, Yue J. Wang, Jonathan Schug, Eseye Feleke, Long Gao, Chengyang Liu, Ali Naji, Benjamin Glaser, Klaus H. Kaestner
Veröffentlicht in:
Molecular Metabolism, Ausgabe 42, 2020, Seite(n) 101057, ISSN 2212-8778
Herausgeber:
Elsevier GmbH
DOI:
10.1016/j.molmet.2020.101057
Autoren:
Luca Tosti, Yan Hang, Olivia Debnath, Sebastian Tiesmeyer, Timo Trefzer, Katja Steiger, Foo Wei Ten, Sören Lukassen, Simone Ballke, Anja A. Kühl, Simone Spieckermann, Rita Bottino, Naveed Ishaque, Wilko Weichert, Seung K. Kim, Roland Eils, Christian Conrad
Veröffentlicht in:
Gastroenterology, Ausgabe 160/4, 2021, Seite(n) 1330-1344.e11, ISSN 0016-5085
Herausgeber:
W. B. Saunders Co., Ltd.
DOI:
10.1053/j.gastro.2020.11.010
Autoren:
Orit Rozenblatt-Rosen, Jay W. Shin, Jennifer E. Rood, Anna Hupalowska, Aviv Regev, Holger Heyn
Veröffentlicht in:
Nature Biotechnology, Ausgabe 39/2, 2021, Seite(n) 149-153, ISSN 1087-0156
Herausgeber:
Nature Publishing Group
DOI:
10.1038/s41587-020-00812-4
Autoren:
Robert Lorenz Chua, Soeren Lukassen, Saskia Trump, Bianca P. Hennig, Daniel Wendisch, Fabian Pott, Olivia Debnath, Loreen Thürmann, Florian Kurth, Maria Theresa Völker, Julia Kazmierski, Bernd Timmermann, Sven Twardziok, Stefan Schneider, Felix Machleidt, Holger Müller-Redetzky, Melanie Maier, Alexander Krannich, Sein Schmidt, Felix Balzer, Johannes Liebig, Jennifer Loske, Norbert Suttorp, Jür
Veröffentlicht in:
Nature Biotechnology, Ausgabe 38/8, 2020, Seite(n) 970-979, ISSN 1087-0156
Herausgeber:
Nature Publishing Group
DOI:
10.1038/s41587-020-0602-4
Autoren:
Tiesmeyer, Sebastian; Sahay, Shashwat; Müller-Bötticher, Niklas; Eils, Roland; Mackowiak, Sebastian D.; Ishaque, Naveed
Veröffentlicht in:
Frontiers in Genetics, section: Computational Genomics, Ausgabe 1, 2022, ISSN 1664-8021
Herausgeber:
Frontiers Media
DOI:
10.3389/fgene.2022.785877
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