DOI: 10.5061/dryad.2280gb612
title: Data from: Molecular and cellular dynamics of the developing human neocortex

description: The development of the human neocortex is a highly dynamic process and
 involves complex cellular trajectories controlled by cell-type-specific
 gene regulation. Here, we collected paired single-nucleus chromatin
 accessibility and transcriptome data from 38 human neocortical samples
 encompassing both the prefrontal cortex and primary visual cortex. These
 samples span five main developmental stages, ranging from the first
 trimester to adolescence. In parallel, we performed spatial transcriptomic
 analysis on a subset of the samples to illustrate spatial organization and
 intercellular communication. This atlas enables us to catalog cell type-,
 age-, and area-specific gene regulatory networks underlying neural
 differentiation. Moreover, combining single-cell profiling, progenitor
 purification, and lineage-tracing experiments, we have untangled the
 complex lineage relationships among progenitor subtypes during the
 transition from neurogenesis to gliogenesis in the human neocortex. We
 identified a tripotential intermediate progenitor subtype, termed Tri-IPC,
 responsible for the local production of GABAergic neurons, oligodendrocyte
 precursor cells, and astrocytes. Remarkably, most glioblastoma cells
 resemble Tri-IPCs at the transcriptomic level, suggesting that cancer
 cells hijack developmental processes to enhance growth and heterogeneity.
 Furthermore, by integrating our atlas data with large-scale GWAS data, we
 created a disease-risk map highlighting enriched ASD risk in
 second-trimester intratelencephalic projection neurons. Our study sheds
 light on the gene regulatory landscape and cellular dynamics of the
 developing human neocortex.
description: # Data from: Molecular and cellular dynamics of the developing human
 neocortex at single-cell resolution
 [https://doi.org/10.5061/dryad.2280gb612](https://doi.org/10.5061/dryad.2280gb612) We collected paired single-nucleus chromatin accessibility and transcriptome data (10x Multiome) from the developing human neocortex. We collected MERFISH data (Vizgen MERSCOPE) from the developing human neocortex. We collected scRNA-seq data (10x Flex) from cultured slices treated with and without somatostatin receptor (SSTR) agonists. We collected scRNA-seq data (10x 3' v3.1) from FACS-isolated glial progenitor cells (GPCs) during in vitro differentiation. ## Description of the data and file structure For 10x Multiome data: * The 10x Genomics Cellranger ARC output files, including atac_fragments.tsv.gz and atac_fragments.tsv.gz.tbi, and filtered_feature_bc_matrix.h5 for each sample (38 samples in total). We used GRCh38 Reference - 2020-A-2.0.0 as the reference file. Detailed information and format of these files can be found [here](https://www.10xgenomics.com/support/software/cell-ranger-arc/latest/analysis/fragments-file) and [here](https://www.10xgenomics.com/support/software/cell-ranger-arc/latest/analysis/outputs-h5-matrices). Additional information on these samples can be found in the Supplementary Table 1 of our publication. * A Seurat object containing count matrices, dimension reduction, and metadata from 38 samples in this experiment (snMultiome_atlas_Seurat_object.rds). For MERFISH data (Vizgen MERSCOPE): A Seurat object containing spatial coordinates, count matrices, dimension reduction, and metadata from six samples in this experiment (MERFISH_Seurat__object.rds). For SSTR agonist treatment data (10x Flex): A Seurat object containing count matrices, dimension reduction, and metadata of excitatory neurons from 20 samples in this experiment (SSTR_agonist_treatment_scRNA-seq_EN_Seurat_object.rds). For GPC differentiation data (10x 3' v3.1): * The 10x Genomics Cellranger output (GPC_differentiation_scRNA-seq_filtered_feature_bc_matrix.h5). We used GRCh38 Reference - 2020-A-2.0.0 as the reference file. Detailed information and format of these files can be found [here](https://www.10xgenomics.com/support/software/cell-ranger-arc/latest/analysis/outputs-h5-matrices). * A Seurat object containing count matrices, dimension reduction, and metadata from 9 samples in this experiment (GPC_differentiation_scRNA-seq_Seurat_object.rds). ## Sharing/Access information Links to raw fastq files for snMultiome: * [https://assets.nemoarchive.org/dat-oiif74w](https://assets.nemoarchive.org/dat-oiif74w) Links to original Vizgen output files for MERFISH: * [https://doi.org/10.35077/g.1156](https://doi.org/10.35077/g.1156) Links to interactive data browsers: * [https://cell.ucsf.edu/snMultiome](https://cell.ucsf.edu/snMultiome/) * [https://cellxgene.cziscience.com/collections/ad2149fc-19c5-41de-8cfe-44710fbada73](https://cellxgene.cziscience.com/collections/ad2149fc-19c5-41de-8cfe-44710fbada73) ## Publication If using these data, please consider citing our publication "[Molecular and cellular dynamics of the developing human neocortex](https://www.nature.com/articles/s41586-024-08351-7)". ## Code/Software [https://github.com/complexdisease/Human_Cortex_Dev_Multiome](https://github.com/complexdisease/Human_Cortex_Dev_Multiome)