Lodato, S. & Arlotta, P. Generating neuronal diversity in the mammalian cerebral cortex. Annu. Rev. Cell Dev. Biol. 31, 699–720 (2015).
Greig, L. C., Woodworth, M. B., Galazo, M. J., Padmanabhan, H. & Macklis, J. D. Molecular logic of neocortical projection neuron specification, development and diversity. Nat. Rev. Neurosci. 14, 755–769 (2013).
Yuzwa, S. A. et al. Developmental emergence of adult neural stem cells as revealed by single-cell transcriptional profiling. Cell Rep. 21, 3970–3986 (2017).
Frazer, S. et al. Transcriptomic and anatomic parcellation of 5-HT3AR expressing cortical interneuron subtypes revealed by single-cell RNA sequencing. Nat. Commun. 8, 14219 (2017).
Mayer, C. et al. Developmental diversification of cortical inhibitory interneurons. Nature 555, 457–462 (2018).
Bielle, F. et al. Multiple origins of Cajal–Retzius cells at the borders of the developing pallium. Nat. Neurosci. 8, 1002–1012 (2005).
Stickels, R. R. et al. Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2. Nat. Biotechnol. 39, 313–319 (2021).
Biancalani, T. et al. Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with Tangram. Preprint at https://doi.org/10.1101/2020.08.29.272831 (2020).
Kim, E. J., Juavinett, A. L., Kyubwa, E. M., Jacobs, M. W. & Callaway, E. M. Three types of cortical layer 5 neurons that differ in brain-wide connectivity and function. Neuron 88, 1253–1267 (2015).
Tasic, B. et al. Shared and distinct transcriptomic cell types across neocortical areas. Nature 563, 72–78 (2018).
Allen Cell Types Database. http://celltypes.brain-map.org/rnaseq/mouse_ctx-hip_smart-seq (Allen Institute for Brain Science, 2015).
Farrell, J. A. et al. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science 360, eaar3131 (2018).
Arlotta, P. et al. Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo. Neuron 45, 207–221 (2005).
Florio, M. & Huttner, W. B. Neural progenitors, neurogenesis and the evolution of the neocortex. Development 141, 2182–2194 (2014).
Jhas, S. et al. Hes6 inhibits astrocyte differentiation and promotes neurogenesis through different mechanisms. J. Neurosci. 26, 11061–11071 (2006).
Malatesta, P. & Götz, M. Radial glia – from boring cables to stem cell stars. Development 140, 483–486 (2013).
Telley, L. et al. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science 364, eaav2522 (2019).
Llorca, A. et al. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife 8, e51381 (2019).
Guo, C. et al. Fezf2 expression identifies a multipotent progenitor for neocortical projection neurons, astrocytes, and oligodendrocytes. Neuron 80, 1167–1174 (2013).
Gao, P. et al. Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell 159, 775–788 (2014).
Franco, S. J. et al. Fate-restricted neural progenitors in the mammalian cerebral cortex. Science 337, 746–749 (2012).
Zahr, S. K. et al. A translational repression complex in developing mammalian neural stem cells that regulates neuronal specification. Neuron 97, 520–537.e6 (2018).
Thompson, C. L. et al. A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain. Neuron 83, 309–323 (2014).
Molyneaux, B. J. et al. DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex. Neuron 85, 275–288 (2015).
Dixit, A. et al. Perturb-seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell 167, 1853–1866 (2016).
Preissl, S. et al. Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nat. Neurosci. 21, 432–439 (2018).
Ma, S. et al. Chromatin potential identified by shared single-cell profiling of RNA and chromatin. Cell 183, 1103–1116 (2020).
Urquhart, J. E. et al. DMRTA2 (DMRT5) is mutated in a novel cortical brain malformation. Clin. Genet. 89, 724–727 (2016).
Cubelos, B. et al. Cux1 and Cux2 regulate dendritic branching, spine morphology, and synapses of the upper layer neurons of the cortex. Neuron 66, 523–535 (2010).
Lodato, S. et al. Excitatory projection neuron subtypes control the distribution of local inhibitory interneurons in the cerebral cortex. Neuron 69, 763–779 (2011).
Molyneaux, B. J., Arlotta, P., Hirata, T., Hibi, M. & Macklis, J. D. Fezl is required for the birth and specification of corticospinal motor neurons. Neuron 47, 817–831 (2005).
Chen, B., Schaevitz, L. R. & McConnell, S. K. Fezl regulates the differentiation and axon targeting of layer 5 subcortical projection neurons in cerebral cortex. Proc. Natl Acad. Sci. USA 102, 17184–17189 (2005).
Lodato, S. et al. Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons. Nat. Neurosci. 17, 1046–1054 (2014).
Hirata, T. et al. Zinc finger gene fez-like functions in the formation of subplate neurons and thalamocortical axons. Dev. Dyn. 230, 546–556 (2004).
Loo, L. et al. Single-cell transcriptomic analysis of mouse neocortical development. Nat. Commun. 10, 134 (2019).
10x Genomics. Nuclei Isolation for Single Cell ATAC Sequencing. Demonstrated Protocol CG000169 (10x Genomics, 2019).
Fleming, S. J., Marioni, J. C. & Babadi, M. CellBender remove-background: a deep generative model for unsupervised removal of background noise from scRNA-seq datasets. Preprint at https://doi.org/10.1101/791699 (2019).
Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902 (2019).
Kowalczyk, M. S. et al. Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells. Genome Res. 25, 1860–1872 (2015).
Blondel, V. D., Guillaume, J.-L., Lambiotte, R., Lefebvre, E. Fast unfolding of communities in large networks. J. Stat. Mech. P10008 (2008).
McGinnis, C. S., Murrow, L. M. & Gartner, Z. J. DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Syst. 8, 329–337 (2019).
Wolock, S. L., Lopez, R. & Klein, A. M. Scrublet: computational identification of cell doublets in single-cell transcriptomic data. Cell Syst. 8, 281–291 (2019).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Angerer, P. et al. destiny: diffusion maps for large-scale single-cell data in R. Bioinformatics 32, 1241–1243 (2016).
Bergen, V., Lange, M., Peidli, S., Wolf, F. A. & Theis, F. J. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat. Biotechnol. 38, 1408–1414 (2020).
Haghverdi, L., Büttner, M., Wolf, F. A., Buettner, F. & Theis, F. J. Diffusion pseudotime robustly reconstructs lineage branching. Nat. Methods 13, 845–848 (2016).
Cao, J. et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496–502 (2019).
Stuart, T., Srivastava, A., Lareau, C. & Satija, R. Multimodal single-cell chromatin analysis with Signac. Preprint at https://doi.org/10.1101/2020.11.09.373613 (2020).
Dong, M. et al. SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references. Brief. Bioinform. 22, 416–427 (2021).
Tan, Y. & Cahan, P. SingleCellNet: a computational tool to classify single cell RNA-seq data across platforms and across species. Cell Syst. 9, 207–213 (2019).
Yu, G., Wang, L. G., Han, Y. & He, Q. Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284–287 (2012).
DeCoN. http://decon.fas.harvard.edu/pyramidal/ (2014).
Allen Developing Mouse Brain Atlas. http://developingmouse.brain-map.org/ (Allen Institute for Brain Science, 2008).