A single-cell genomics approach integrating gene expression, lineage, and physical interactions

Project Information

IntScOmics

Grant agreement ID: 742225

DOI

10.3030/742225

Project closed

EC signature date 12 September 2017

Start date 1 January 2018

End date 31 December 2022

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 500 000,00

EU contribution

€ 2 500 000,00

Coordinated by

KONINKLIJKE NEDERLANDSE AKADEMIE VAN WETENSCHAPPEN - KNAW
Netherlands

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (15)

Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development

Author(s): M. Sen, D. Mooijman, A. Chialastri, J.C. Boisset, M. Popovic, B. Heindryckx, S.M. Chuva de Sousa Lopes , S.S. Dey, A. van Oudenaarden.
Published in: Nature Communications, Issue 12, 2023, Page(s) 1286, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-21532-6

Integration of multiple lineage measurements from the same cell reconstructs parallel tumor evolution

Author(s): L. Kester, B. de Barbanson, A. Lyubimova, L.T. Chen, V. van der Schrier, A. Alemany, D. Mooijman, J. Peterson-Maduro, J. Drost, J. de Ridder, A. van Oudenaarden.
Published in: Cell Genomics, Issue 2, 2022, Page(s) 100094, ISSN 2666-979X
Publisher: Elsevier
DOI: 10.1016/j.xgen.2022.100096

Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

Author(s): Susanne C. van den Brink, Anna Alemany, Vincent van Batenburg, Naomi Moris, Marloes Blotenburg, Judith Vivié, Peter Baillie-Johnson, Jennifer Nichols, Katharina F. Sonnen, Alfonso Martinez Arias, Alexander van Oudenaarden
Published in: Nature, Issue 582/7812, 2020, Page(s) 405-409, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-020-2024-3

Cell Type Purification by Single-Cell Transcriptome-Trained Sorting

Author(s): Chloé S. Baron, Aditya Barve, Mauro J. Muraro, Reinier van der Linden, Gitanjali Dharmadhikari, Anna Lyubimova, Eelco J.P. de Koning, Alexander van Oudenaarden
Published in: Cell, Issue 179/2, 2019, Page(s) 527-542.e19, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2019.08.006

Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies

Author(s): Nico Battich, Joep Beumer, Buys de Barbanson, Lenno Krenning, Chloé S. Baron, Marvin E. Tanenbaum, Hans Clevers, Alexander van Oudenaarden
Published in: Science, Issue 367/6482, 2020, Page(s) 1151-1156, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aax3072

scChIX-seq infers dynamic relationships between histone modifications in single cells

Author(s): J. Yeung, M. Florescu, P. Zeller, B.A. de Barbanson, M.D. Wellenstein, A. van Oudenaarden.
Published in: Nature Biotechnology, 2023, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-022-01560-3

Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo

Author(s): W. van Leeuwen, M. VanInsberghe, N. Battich, F. Salmén, A. van Oudenaarden, C. Rabouille.
Published in: Cell Rep Methods, Issue 2, 2022, Page(s) 100235, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1016/j.crmeth.2022.100235

Whole-organism clone tracing using single-cell sequencing

Author(s): Anna Alemany, Maria Florescu, Chloé S. Baron, Josi Peterson-Maduro, Alexander van Oudenaarden
Published in: Nature, Issue 556/7699, 2018, Page(s) 108-112, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/nature25969

Single-Cell Transcriptomics Meets Lineage Tracing

Author(s): Lennart Kester, Alexander van Oudenaarden
Published in: Cell Stem Cell, Issue 23/2, 2018, Page(s) 166-179, ISSN 1934-5909
Publisher: Cell Press
DOI: 10.1016/j.stem.2018.04.014

Mapping the physical network of cellular interactions

Author(s): Jean-Charles Boisset, Judith Vivié, Dominic Grün, Mauro J. Muraro, Anna Lyubimova, Alexander van Oudenaarden
Published in: Nature Methods, Issue 15/7, 2018, Page(s) 547-553, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-018-0009-z

Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics

Author(s): Andrea Attardi, Timothy Fulton, Maria Florescu, Gopi Shah, Leila Muresan, Martin O. Lenz, Courtney Lancaster, Jan Huisken, Alexander van Oudenaarden, Benjamin Steventon
Published in: Development, Issue 145/21, 2018, Page(s) dev166728, ISSN 0950-1991
Publisher: The Company of Biologists Ltd.
DOI: 10.1242/dev.166728

High-throughput total RNA sequencing in single cells using VASA-seq

Author(s): Fredrik Salmen; Joachim De Jonghe; Tomasz S. Kaminski; Anna Alemany; Guillermo E. Parada; Joe Verity-Legg; Ayaka Yanagida; Timo N. Kohler; Nicholas Battich; Floris van den Brekel; Anna L. Ellermann; Alfonso Martinez Arias; Jennifer Nichols; Martin Hemberg; Florian Hollfelder; Alexander van Oudenaarden
Published in: Nature Biotechnology. Nature Publishing Group, Issue 1, 2022, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.17863/cam.91785

Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis

Author(s): P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden.
Published in: Nature Genetics, Issue 55, 2023, Page(s) 333-345, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-022-01260-3

Single-cell Ribo-seq reveals cell cycle-dependent translational pausing

Author(s): M. VanInsberghe, J. van den Berg, A. Andersson-Rolf, H. Clevers, A. van Oudenaarden.
Published in: Nature, Issue 597, 2021, Page(s) 561-565, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-021-03887-4

An in vitro model of early anteroposterior organization during human development

Author(s): Naomi Moris, Kerim Anlas, Susanne C. van den Brink, Anna Alemany, Julia Schröder, Sabitri Ghimire, Tina Balayo, Alexander van Oudenaarden, Alfonso Martinez Arias
Published in: Nature, Issue 582/7812, 2020, Page(s) 410-415, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-020-2383-9