A spatial atlas of 4,434,020 cells resolving how the cellular architecture of Broca's area and the primary motor cortex is laid down across the developing human brain — from neonate to adult.
Figure 1Brodmann-area microdissections of the primary motor and Broca's areas were serially sectioned and profiled by Xenium spatial transcriptomics — 56 sections at 460-plex (3,512,533 cells) and 12 sections at 5,000-plex (921,487 cells). Cells were annotated by snRNA-seq label transfer into 69 fine-grained types, and cortical layers were resolved by marker-gene annotation and quantified across areas, layers and developmental stages.
Sixty-nine transcriptomic cell types across the major cortical classes, mapped in situ across five cortical layers in two Brodmann areas and four developmental stages.
Fig. 3–4The major cortical classes resolved into 69 fine-grained cell types via snRNA-seq label transfer, and localised across five cortical layers with marker-gene annotation.
All datasets, figures and analysis notebooks are openly available. Download the processed objects, browse the cells interactively, or reproduce the analysis end to end.
Processed spatial transcriptomic AnnData objects, ready for scanpy / squidpy.
1Department of Neurology, University of California, San Francisco, CA, USA
2Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, UCSF, CA, USA
3Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, India
4Wellcome Sanger Institute, Hinxton, Cambridge, UK
5Department of Anatomy, UCSF, San Francisco, CA, USA
6Department of Pediatrics, UCSF, San Francisco, CA, USA
7Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
8Department of Pathology, UCSF, San Francisco, CA, USA
9Institute of Computational Biology, Helmholtz Munich, Germany
10TUM School of Computation, Information and Technology, TU Munich, Germany
11TUM School of Life Sciences, Technical University of Munich, Germany
12Weill Institute for Neurosciences, UCSF, CA, USA
13Departments of Pediatrics and Neurosurgery, UCSF, San Francisco, CA, USA
14Newborn Brain Research Institute, UCSF, San Francisco, CA, USA
15Department of Pediatrics, UCSF, San Francisco, CA, USA
16Department of Neurological Surgery, UCSF, CA, USA
17Departments of Pediatrics and Neurosurgery, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA
18Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
19Department of Psychiatry and Behavioral Sciences, UCSF, San Francisco, CA, USA