During the first year, work was severely disrupted by the COVID pandemic. Nevertheless, the project has made good progress. In WP3, Linnarsson group has generated large datasets from human fetal brain, both single-cell RNA-seq and ATAC-seq (250k cells). We have also now begun to generate Multiome data, combining RNA and ATAC, which will aid integration across modalities. In WP4, the Lein group focused on experiments to optimize tissue handling and nuclei isolation from human brain tissues derived from aged and Alzheimer’s disease human tissue donors. In WP5, the Amit and Treutlein groups have developed and calibrated advanced experimental models of human microglia in different organoid model systems. We are currently comparing these models to data we collected from human microglia in different stages of development with an aiming of using the most relevant model for perturbation experiments. In WP6, the Tanay group worked toward parametric manifold models and implementation of spatio temporal data analysis schemes over them. Application of Metaman and the network flows approach to data on gastrulation and initial deployment of the new tools for understanding Braintime data demonstrate the remarkable potential of these approach, in particular given very large scale data.
In the final period, the project completed data acquisition for both fetal, adult, diseased and ageing human brain, as well as organoids, and the preparation of several manuscripts for submission. We completed the atlas of the developing brain comprising more than 1.6 million (RNA) and 500,000 (ATAC, Multiome) cells. A first manuscript is currently in revision. Similarly, we completed a single-cell survey of adult, ageing and disease human brains. We performed spatial RNA detection using a greatly improved method (EEL FISH) capable of detecting up to 440 genes in large tissue sections (WP3). We developed and optimized methods for computational modelling of cellular manifolds (WP6) and corresponding methods for genetic lineage tracing (e.g. iTracer, WP5), as well as applying methods for cell-cell interaction analysis (PIC-seq, WP5). We further developed new and improved strategy for mapping query scRNA-seq on atlases, and we developed a scalable and interactive browser enabling thew community to explore our datasets.
Overall, these results meant that the key objectives were achieved.No exploitable intellectual property was generated during the project. Tools, data and results were shared without restriction (beyond what was required for protecting the privacy of donors). Dissemination activities included a large number of attended conferences, including some co-organized by partners; preprints submitted to bioRxiv; scientific publications; scoail media and web presence.
