Human Pediatric Brain Atlas
Research resource Xenium spatial transcriptomics · Human cortex · Development

A multimodal interrogation of Broca's area in the pediatric and adult human brain

J. Moriano*, T. Mukhtar*, J. T. H. Lee*, F. Memi*, J. Augustin*, R. Leonard, J. Asfouri, I-L. Lu, C. Siebert, J. J-Y. Choi, G. Zuo, Y. Chang, S. Makarchuk, E. Jin, M. Prete, S. Wang, Q. Bi, Y. Hao, L. Tuck, C. Tudor, V. Brito Pereira, H. M. Chan, J. Halliwell, B. Rumney, H. Anderson, A. Ramsey, F. Theis, M. Paredes, X. Piao, E. E. Crouch, A. Alvarez-Buylla, D. Rowitch, E. J. Huang, T. J. Nowakowski#, O. A. Bayraktar#, A. Kriegstein#

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.

4,434,020
cells profiled
69
cell types
4
donors · 5mo–36y
2
cortical areas
460 / 5k
plex panels

From serial sections to a spatial map of cortical development

Study design: Brodmann-area microdissections of motor and Broca's area serially sectioned and profiled with 460-plex and 5,000-plex Xenium spatial transcriptomics across four developmental stages, annotated by snRNA-seq label transfer into 69 fine-grained cell types and five cortical layers.

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.

A fine-grained spatial atlas of the human cortex

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.

Excitatory neuronsIT · ET · CT · NP · L6b
Inhibitory neuronsPVALB · SST · VIP · LAMP5 · PAX6 · SNCG
OligodendrocytesST18 · MOBP
OPCPDGFRA · PTPRZ1
AstrocytesGFAP · HPSE2
Microglia & immuneDOCK8 · SKAP1
Vascularendothelial · pericyte · VLMC

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.

Donor cohort
4 DONORS
3
pediatric (5mo · 4y · 9y)
1
adult (36y)
3
developmental stages
Ages span the neonatal, childhood and adult stages, sampled from the primary motor area and Broca's area of the human cortex.

Data & code availability

All datasets, figures and analysis notebooks are openly available. Download the processed objects, browse the cells interactively, or reproduce the analysis end to end.

Authors & affiliations

Juan Moriano1,2,*, Tanzila Mukhtar1,2,3,*, Jimmy Tsz Hang Lee4,*, Fani Memi4,*, Jonathan Augustin1,2,*, Rachel Leonard5, Joseph Asfouri5, I-Ling Lu2,6, Clara Siebert1,2,7, Jennifer Ja-Yoon Choi8,18, Guolong Zuo1,2, Yinshui Chang4, Stanislaw Makarchuk4, Elina Jin4, Martin Prete4, Shaohui Wang1,2, Qiuli Bi1,2, Yuhan Hao16, Liz Tuck4, Catherine Tudor4, Vanessa Brito Pereira4, Hon Man Chan4, Jasmine Halliwell4, Benjamin Rumney4, Holly Anderson4, Arren Ramsey8, Fabian Theis9,10,11, Mercedes Paredes1,2,12, Xianhua Piao2,13,14, Elizabeth E. Crouch2,15, Arturo Alvarez-Buylla2,16, David Rowitch2,6,17, Eric J. Huang8,18, Tomasz J. Nowakowski2,5,12,16,19,#, Omer Ali Bayraktar4,#, Arnold Kriegstein1,2,#

* Equal contribution  ·  # Corresponding authors: tomasz.nowakowski@ucsf.edu, ob5@sanger.ac.uk, arnold.kriegstein@ucsf.edu

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

Citation

Preprint
Moriano J, Mukhtar T, Lee JTH, Memi F, Augustin J, et al. A multimodal interrogation of Broca's area in the pediatric and adult human brain. bioRxiv (2026). doi: 10.64898/2026.07.22.739934