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. 2022 Dec 12;13:7671. doi: 10.1038/s41467-022-34975-2

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a Schematic of macrodissection and sequencing approach to study germinal matrix (GM, n = 15) and cortical plate (CP, n = 15) development in the second and third trimesters (17–41 gw) with corresponding adult brain regions, SVZ (n = 3) and CX (n = 3). b, c UMAP plots for all prenatal samples integrated by anatomical region: GM (b) and CP (c). Clusters (left) are colored by cell type annotation (right). d, e Heatmaps of log-normalized average gene expression per cluster, showing selected canonical marker genes (rows) used to assign cell identity to each cluster (columns) in (b) and (c), respectively. Clusters are grouped and colored by cell identity. f Stacked bar plots of stage-normalized cell type proportions in the GM (top) and CP (bottom), showing changes in the factions of glia and neurons over four defined stages of prenatal development: stage 1 (17–20 gw), stage 2 (20–24 gw), stage 3 (24–28 gw), stage 4 (31–41gw). Normalization is based on the total number of nuclei assigned to a cell type. CPN, SPN, and CRN included as part of EN, MSN included as part of IN, UD not included. g UMAP display of cell cycle phase annotations within the integrated GM (top) and CP (bottom), highlighting actively cycling cells as TAC. h Stacked bar plot of TAC state cell type proportions in GM (top) and CP (bottom). Cell type identity is based on prediction scores from cell type signatures in (b) and (c). Source data for (f, h) are provided as a Source Data file. See also Supplementary Figs. 1–3. TAC transit-amplifying cell/cycling progenitor, RG radial glia, oRG outer radial glia, tRG truncated radial glia, EPD ependymal cell, AC astrocyte, AC-f fibrous astrocyte, AC-p protoplasmic astrocyte, gIPC glial intermediate progenitor cell, OPC oligodendrocyte progenitor cell, preOL premyelinating/early myelinating BCAS1+ oligodendrocyte, OL oligodendrocyte, nIPC neuronal intermediate progenitor cell, mIPC multipotent intermediate progenitor cell, UD undefined, MSN medium spiny neuron, EN excitatory neuron, CPN cortical projection neuron, SPN subplate neuron, CRN Cajal Retzius cell, IN interneuron, MG microglia, BVC blood vessel cell, L2/3, L4, L5/6 neocortical layers 2/3, 4, 5/6, GM or G prenatal germinal matrix, CP prenatal cortical plate or choroid plexus, SVZ adult subventricular zone, CN caudate nucleus, LV lateral ventricles, WM white matter, CX adult neocortex, gw gestational weeks, yr years.