Molecular atlas of the brain across the human lifespan

Project Information

BRAINTIME

Grant agreement ID: 874606

DOI 10.3030/874606

Project closed

EC signature date 6 December 2019

Start date 1 January 2020

End date 30 June 2022

Funded under

• SOCIETAL CHALLENGES - Health, demographic change and well-being

Total cost € 4 328 051,25

EU contribution € 4 328 051,25

Coordinated by

KAROLINSKA INSTITUTET
Sweden

Publications

Peer reviewed articles (15)

Charting human development using a multi-endodermal organ atlas and organoid models

Author(s): Qianhui Yu; Umut Kilik; Emily M. Holloway; Yu-Hwai Tsai; Christoph Harmel; Angeline Wu; Joshua H. Wu; Michael Czerwinski; Charlie Childs; Zhisong He; Meghan M. Capeling; Sha Huang; Ian A. Glass; Peter D.R. Higgins; Barbara Treutlein; Jason R. Spence; J. Gray Camp
Published in: Cell, 184 (12), Issue 00928674, 2021, Page(s) 3281-3298, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2021.04.028

Comparison of seven single cell whole genome amplification commercial kits using targeted sequencing

Author(s): Tamir Biezuner, Ofir Raz, Shiran Amir, Lilach Milo, Rivka Adar, Yael Fried, Elena Ainbinder, and Ehud Shapiro
Published in: Scientific Reports, Issue 20452322, 2021, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-96045-9

Lineage recording in human cerebral organoids

Author(s): Zhisong He; Ashley Maynard; Akanksha Jain; Tobias Gerber; Rebecca Petri; Hsiu-Chuan Lin; Malgorzata Santel; Kevin Ly; Jean-Samuel Dupré; Leila Sidow; Fatima Sanchis Calleja; Sophie M. J. Jansen; Stephan Riesenberg; J. Gray Camp; Barbara Treutlein
Published in: Nature Methods, Issue 15487091, 2021, Page(s) 90-99, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.3929/ethz-b-000524021

Single-cell RNA-sequencing of mammalian brain development: insights and future directions

Author(s): Elin Vinsland , Sten Linnarsson
Published in: Development, Issue 09501991, 2022, ISSN 0950-1991
Publisher: The Company of Biologists Ltd.
DOI: 10.1242/dev.200180

Resolving Neurodevelopmental and Vision Disorders Using Organoid Single-Cell Multi-omics.

Author(s): Giovanna Brancati; Barbara Treutlein; J. Gray Camp
Published in: Neuron, 107 (6), Issue 08966273, 2020, Page(s) 1000-1013, ISSN 0896-6273
Publisher: Cell Press
DOI: 10.1016/j.neuron.2020.09.001

A single-embryo, single-cell time-resolved model for mouse gastrulation.

Author(s): Mittnenzweig M, Mayshar Y, Cheng S, Ben-Yair R, Hadas R, Rais Y, Chomsky E, Reines N, Uzonyi A, Lumerman L, Lifshitz A, Mukamel Z, Orenbuch AH, Tanay A*, Stelzer Y*.
Published in: Cell, Issue 00928674, 2021, Page(s) 2825-2842, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2021.04.004

Evolutionary cell type mapping with single-cell genomics

Author(s): Tanay A*, Sebé-Pedrós A*.
Published in: Trends in Genetics, Issue 01689525, 2021, Page(s) 919-932, ISSN 0168-9525
Publisher: Elsevier BV
DOI: 10.1016/j.tig.2021.04.008

Retrospective cell lineage reconstruction in humans by using short tandem repeats

Author(s): Liming Tao, Ofir Raz, Zipora Marx, Manjusha S.Ghosh, Sandra Huber, Julia Greindl-Junghans, Tamir Biezuner, Shiran Amir, Lilach Milo, Rivka Adar, Ron Levy, Amos Onn, NoaChapal-Ilan, Veronika Berman, Asaf Ben Arie, Guy Rom, Bara Oron, Ruth Halaban, Zbigniew T.Czyz, Melanie Werner-Klein…Ehud Shapiro
Published in: Cell Reports Methods, Issue 26672375, 2021, ISSN 2667-2375
Publisher: Elsevier
DOI: 10.1016/j.crmeth.2021.100054

The Organoid Cell Atlas

Author(s): Christoph Bock, Michael Boutros, J. Gray Camp, Laura Clarke, Hans Clevers, Juergen A. Knoblich, Prisca Liberali, Aviv Regev, Anne C. Rios, Oliver Stegle, Hendrik G. Stunnenberg, Sarah A. Teichmann, Barbara Treutlein, Robert G. J. Vries & the Human Cell Atlas ‘Biological Network’ Organoids
Published in: Nature Biotechnology, Issue 10870156, 2021, Page(s) 13-17, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-020-00762-x

Spatial transcriptomic and single-nucleus analysis reveals heterogeneity in a gigantic single-celled syncytium

Author(s): Nico Schramma; Cristina Loureiro; Tobias Gerber; Siyu Chen; Akanksha Jain; Anne Weber; Anne Weigert; Malgorzata Santel; Karen Alim; Barbara Treutlein; J Gray Camp
Published in: eLife, Issue 2050084X, 2022, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.69745

Metacell-2: a divide-and-conquer metacell algorithm for scalable scRNA-seq analysis.

Author(s): Ben-Kiki O, Bercovich A, Lifshitz A, Tanay A
Published in: Genome Biology, Issue 1474760X, 2022, ISSN 1474-760X
Publisher: Springer Nature
DOI: 10.1186/s13059-022-02667-1

Inferring and perturbing cell fate regulomes in human brain organoids

Author(s): Jonas Simon Fleck, Sophie Martina Johanna Jansen, Damian Wollny, Fides Zenk, Makiko Seimiya, Akanksha Jain, Ryoko Okamoto, Malgorzata Santel, Zhisong He, J. Gray Camp& Barbara Treutlein
Published in: Nature, Issue 00280836, 2022, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-022-05279-8

The intrinsic and extrinsic effects of TET proteins during gastrulation

Author(s): Saifeng Cheng, Markus Mittnenzweig, Yoav Mayshar, Aviezer Lifshitz, Marko Dunjić, Yoach Rais, Raz Ben-Yair, Stephanie Gehrs, Elad Chomsky, Zohar Mukamel, Hernan Rubinstein, Katharina Schlereth, Netta Reines, Ayelet-Hashahar Orenbuch, Amos Tanay, Yonatan Stelzer
Published in: Cell, Issue 00928674, 2022, Page(s) 3169-3185, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2022.06.049

NGN2 induces diverse neuron types from human pluripotency

Author(s): "H.-C. Lin*, Z. He*, S. Ebert*, M. Schörnig, M. Santel, A. Weigert, W. Hevers, N. N. Kasri, E. Taverna, J. G. Camp#, B. Treutlein#,"
Published in: Stem Cell Reports, Issue 22136711, 2021, Page(s) 2118-2127, ISSN 2213-6711
Publisher: Cell Press
DOI: 10.1016/j.stemcr.2021.07.006

Whole-Genome Amplification—Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs

Author(s): Ofir Raz; Liming Tao; Tamir Biezuner; Tzipy Marx; Yaara Neumeier; Narek Tumanyan; Ehud Shapiro
Published in: International Journal of Molecular Sciences; Volume 23; Issue 11; Pages: 6161, Issue 14220067, 2022, Page(s) 6161, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23116161

Non-peer reviewed articles (1)

Multimodal spatiotemporal phenotyping of human organoid development

Author(s): "P. Wahle*, G. Brancati*, C. Harmel*, Z. He*, G. Gut, A. Santos, Q. Yu, P. Noser, J.S. Fleck, B. Gjeta, D. Pavlinić, S. Picelli, M. Hess, G. Schmidt, T. Lummen, Y. Hou, P. Galliker, M. Renner, L. Pelkmans#, B. Treutlein#, J.G. Camp"
Published in: BioRxiv, Issue 26928205, 2022, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.03.16.484396