BICAN: Cell Census of Developing Brain

Chromatin accessibility during human first-trimester neurodevelopment

core

Authors

Camiel C. A. Mannens, Lijuan Hu, Peter Lönnerberg, Marijn Schipper, Caleb C. Reagor, Xiaofei Li, Xiaoling He, Roger A. Barker, Erik Sundström, Danielle Posthuma & Sten Linnarsson

Citation

Mannens, C.A., et al. Chromatin accessibility during human first-trimester neurodevelopment. Nature (2024). https://doi.org/10.1038/s41586-024-07234-1

Summary

We have profiled gene expression and chromatin accessibility across the brain of 26 first-trimester fetal samples (6-13 p.c.w), identifying region-specific cell types and temporal gradients in chromatin accessibility during the early phases of neurodvelopment. In particular, we used machine learning to identify key transcription factors that drive the accessibility of enhancers in distinct neuron subtypes.

Nature Collection

Mannens et al., Nature

Data and Tools

Resource Name	Resource URL	Description
Chromograph	https://github.com/linnarsson-lab/chromograph	Code Repository: Chromograph code for data analysis.
DELAY	https://github.com/calebclayreagor/DELAY	Code Repository: DELAY for Depicting Lagged causalitY across single-cell trajectories for accurate gene-regulatory inference.
CATlas web browser	https://catlas.org/humanbraindev/	Data exploration: Human Brain Development 10x-multiome data from 526,094 nuclei
European Genome Phenome Archive	https://www.ega-archive.org/studies/EGAS00001007472	Data Download: human scATAC-seq and combined scRNA-seq from 116 single cell ATAC runs and 23 single cell multiome runs.