Radial glia (RG), intermediate progenitor cells (IPC), and excitatory neurons (N) were selected from published single-cell RNA sequencing data of human and mouse developing neocortex and of human cortical organoids (see below). Data were integrated by species and condition so that any bias in gene expression due to protocol or sequencing depth was overcome.

To compare gene expression dynamics between species and conditions, ordinal regression models were built for each species / condition as follow:

• Differentiation model: predicting the cell type (from RG to IPC to N) across ages
• Age models: for each cell type, the age of the cells was predicted, from early to late corticogenesis / in vitro time.

We used the prediction scores from these models to organize the cells in 2 dimensions based on their predicted age (x axis) and differentiation (y axis), and plotted gene expression after 200 neighbor - smoothing. Correlations between gene expression landscapes from human, mouse and organoids were then calculated.

For more details on the methods, see REF.

In vivo: embryonic neocortical cells

Human: from post-conception week (pcw) 12 to 24

Kn17
Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex. Nowakowski et al., Science 2017.
DOI: 10.1126/science.aap8809
Cells selected:
Region: parietal cortex; Age: pcw 16, 20; Types: RG, IPC, N
Protocol: single cell dissociation using papain; Fluidigm C1; Illumina HiSeq2500

Kb21
An atlas of cortical arealization identifies dynamic molecular signatures. Bhaduri et al., Nature 2021.
DOI: 10.1038/s41586-021-03910-8
Cells selected:
Region: parietal; Age: pcw 12, 15, 16, 17, 18, 20, 23; Types: RG, IPC, N
Protocol: single cell dissociation using papain; 10X Genomics; Illumina NovaSeq S4

Pt21
Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution. Trevino et al., Cell 2021.
DOI: 10.1016/j.cell.2021.07.039
Cells selected:
Age: pcw 16, 20, 21, 24; Types: RG, IPC, N
Protocol: single cell dissociation using papain; 10X Genomics v3

Mouse: from embryonic day (E) 12 to 17

My17
Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling. Yuzwa et al., Cell Rep 2017.
DOI: 10.1016/j.celrep.2017.12.017
Cells selected:
Age: E13, 15, 17; Types: RG, IPC, N
Protocol: single cell mechanical dissociation in cortical precursor medium; Drop-seq; Illumina NextSeq500

Jt19
Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Telley et al., Science 2019.
DOI: 10.1126/science.aav2522
Cells selected:
Region: prospective somatosensory cortex; Age: E12, 13, 14, 15, 16; Types: RG, N
Protocol: single cell dissociation using trypsin; C1 Fluidigm; Illumina HiSeq2500

Ad21
Molecular logic of cellular diversification in the mouse cerebral cortex. Di Bella et al., Nature 2021.
DOI: 10.1038/s41586-021-03670-5
Cells selected:
Region: prospective somatosensory cortex; Age: E12, 13, 14, 15, 16; Types: RG, IPC, N
Protocol: single cell dissociation using papain; 10X Genomics v2; Illumina HiSeq or NovaSeq

LMl21
Molecular architecture of the developing mouse brain. La Manno et al., Nature 2021.
DOI: 10.1038/s41586-021-03775-x
Cells selected:
Region: dorsal forebrain; Age: E12, 13, 14, 15, 16, 17; Types: RG, IPC, N
Protocol: single cell dissociation using trypsin + papain; 10X Genomics v1; Illumina HiSeq

In vitro: human cortical organoids

Kp19: from 2 to >8 months in vitro (miv)
Establishing cerebral organoids as models of human-specific brain evolution. Pollen et al., Cell 2019.
DOI: 10.1016/j.cell.2019.01.017
Cells selected:
Age: miv 2-3, 3-4, 4-5, 5-6, >8; Types: RG, IPC, N
Protocol: single cell dissociation using papain; C1 Fluidigm; Illumina HiSeq 2500
Culture protocol: Kadoshima et al., PNAS 2013 (DOI: 10.1073/pnas.1315710110)

Av19: from 2 to 6 miv
Individual brain organoids reproducibly form cell diversity of the human cerebral cortex. Velasco et al., Nature 2019.
DOI: 10.1038/s41586-019-1289-x
Cells selected:
Age: miv 2-3, 5-6; Types: RG, IPC, N
Protocol: single cell dissociation using papain; 10X Genomics v2; Illumina NextSeq 500
Culture protocol: Kadoshima et al., PNAS 2013 (DOI: 10.1073/pnas.1315710110)

Pt20
Synthetic analyses of single-cell transcriptomes from multiple brain organoids and fetal brain. Tanaka et al., Cell Rep 2020.
DOI: 10.1016/j.celrep.2020.01.038
Cells selected:
Age: miv 1-2, 2-3, 3-4, 6-7; Types: RG, IPC, N

Source	Culture protocol
Fiddes et al., Cell 2018 DOI: 10.1016/j.cell.2018.03.051	Eiraku et al., Cell Stem Cell 2008 DOI: 10.1016/j.stem.2008.09.002
Birey et al., Nature 2017 DOI: 10.1038/nature22330	Pasca et al., Nat Methods 2015 DOI: 10.1038/Nmeth.3415
Madhavan et al., Nat Methods 2018 DOI: 10.1038/s41592-018-0081-4
Trujillo et al., Cell Stem Cell 2019 DOI: 10.1016/j.stem.2019.08.002
Xiang et al., Cell Stem Cell 2017 DOI: 10.1016/j.stem.2017.07.007	Kadoshima et al., PNAS 2013 DOI: 10.1073/pnas.1315710110
Quadrato et al., Nature 2017 DOI: 10.1038/nature22047	Lancaster et al., Nature 2013 DOI: 10.1038/nature12517
Giandomenico et al., Nat Neurosci 2019 DOI: 10.1038/s41593-019-0350-2

Data and code to reproduce this research work is available at Open Science Framework and GitHub.