R/NormalBrainSignatures3.R
NormalBrainSignatures3.RdSignatures were derived from 7 publications (below). Clusters were taken from each publication, and differentially expressed genes were computed for each cluster using scalop::dea. If the publication had subclusters, then scalop::dea was computed for that subcluster against other cells in the same cluster, rather than across the whole dataset.
NormalBrainSignatures3list of character vectors
(1) Nowakowski, T. J., Bhaduri, A., Pollen, A. A., Alvarado, B., Mostajo-Radji, M. A., Di Lullo, E., … Kriegstein, A. R. (2017). Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex. Science, 358(6368), 1318–1323.
(2) Polioudakis, D., de la Torre-Ubieta, L., Langerman, J., Elkins, A. G., Shi, X., Stein, J. L., … Geschwind, D. H. (2019). A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation. Neuron, 103(5), 785-801.e8.
(3) Habib, N., Li, Y., Heidenreich, M., Swiech, L., Avraham-Davidi, I., Trombetta, J. J., … Regev, A. (2016). Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons. Science, 353(6302), 925–928.
(4) Campbell, J. N., Macosko, E. Z., Fenselau, H., Pers, T. H., Lyubetskaya, A., Tenen, D., … Tsai, L. T. (2017). A molecular census of arcuate hypothalamus and median eminence cell types. Nature Neuroscience, 20(3), 484–496.
(5) Schaum, N., Karkanias, J., Neff, N. F., May, A. P., Quake, S. R., Wyss-Coray, T., … Weissman, I. L. (2018). Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature, 562(7727), 367–372.
(6) Velmeshev, D., Schirmer, L., Jung, D., Haeussler, M., Perez, Y., Mayer, S., … Kriegstein, A. R. (2019). Single-cell genomics identifies cell type–specific molecular changes in autism. Science, 364(6441), 685–689.
(7) Luo, C., Liu, H., Xie, F., Armand, E. J., Siletti, K., Bakken, T. E., … Ecker, J. R. (2019). Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants. BioRxiv, 2019.12.11.873398.