References
Belmonte, M.F., Kirkbride, R.C., Stone, S.L., Pelletier, J.M., Bui, A.Q., Yeung, E.C., Hashimoto, M., Fei, J., Harada, C.M., Munoz, M.D., 2013. Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed. Proceedings of the National Academy of Sciences 110, E435–E444.
Cuperus, J.T., 2022. Single-cell genomics in plants: current state, future directions, and hurdles to overcome. Plant Physiology 188, 749–755.
De Chaumont, F., Dallongeville, S., Chenouard, N., Hervé, N., Pop, S., Provoost, T., Meas-Yedid, V., Pankajakshan, P., Lecomte, T., Le Montagner, Y., 2012. Icy: an open bioimage informatics platform for extended reproducible research. Nature methods 9, 690–696.
Fuchs, M., Lohmann, J.U., 2020. Aiming for the top: non-cell autonomous control of shoot stem cells in Arabidopsis. Journal of plant research 133, 297–309.
Guo, X., Park, C.H., Wang, Z.-Y., Nickels, B.E., Dong, J., 2021. A spatiotemporal molecular switch governs plant asymmetric cell division. Nature plants 7, 667–680.
Kahle, D.J., Wickham, H., 2013. ggmap: spatial visualization with ggplot2. R J. 5, 144.
Kajala, K., Gouran, M., Shaar-Moshe, L., Mason, G.A., Rodriguez-Medina, J., Kawa, D., Pauluzzi, G., Reynoso, M., Canto-Pastor, A., Manzano, C., 2021. Innovation, conservation, and repurposing of gene function in root cell type development. Cell 184, 3333-3348. e19.
Libault, M., Pingault, L., Zogli, P., Schiefelbein, J., 2017. Plant systems biology at the single-cell level. Trends in Plant Science 22, 949–960.
Nguyen, S.T., McCurdy, D.W., 2015. High-resolution confocal imaging of wall ingrowth deposition in plant transfer cells: Semi-quantitative analysis of phloem parenchyma transfer cell development in leaf minor veins of Arabidopsis. BMC Plant Biology 15, 1–14.
Rahni, R., Birnbaum, K.D., 2019. Week-long imaging of cell divisions in the Arabidopsis root meristem. Plant Methods 15, 1–14.
Ron, M., Kajala, K., Pauluzzi, G., Wang, D., Reynoso, M.A., Zumstein, K., Garcha, J., Winte, S., Masson, H., Inagaki, S., 2014. Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. Plant physiology 166, 455–469.
Shahan, R., Hsu, C.-W., Nolan, T.M., Cole, B.J., Taylor, I.W., Greenstreet, L., Zhang, S., Afanassiev, A., Vlot, A.H.C., Schiebinger, G., 2022. A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants. Developmental cell 57, 543-560. e9.
Shi, D., Jouannet, V., Agustí, J., Kaul, V., Levitsky, V., Sanchez, P., Mironova, V.V., Greb, T., 2021. Tissue-specific transcriptome profiling of the Arabidopsis inflorescence stem reveals local cellular signatures. The Plant Cell 33, 200–223.
Sotta, N., Fujiwara, T., 2017. Preparing thin cross sections of Arabidopsis roots without embedding. BioTechniques 63, 281–283.
Taiz, L., Zeiger, E., Møller, I.M., Murphy, A., 2015. Plant physiology and development. Sinauer Associates Incorporated.
Torres-Martinez, H.H., Rodriguez-Alonso, G., Shishkova, S., Dubrovsky, J.G., 2019. Lateral root primordium morphogenesis in angiosperms. Frontiers in plant science 10, 206.
Tsukaya, H., 2013. Leaf development. The Arabidopsis Book/American Society of Plant Biologists 11.
Vanhaeren, H., Gonzalez, N., Inzé, D., 2015. A journey through a leaf: phenomics analysis of leaf growth in Arabidopsis thaliana. The Arabidopsis Book/American Society of Plant Biologists 13.
Wendrich, J.R., Weijers, D., 2013. The A rabidopsis embryo as a miniature morphogenesis model. New Phytologist 199, 14–25.
Wickham, H., 2011. ggplot2. Wiley interdisciplinary reviews: computational statistics 3, 180–185.
Winter, D., Vinegar, B., Nahal, H., Ammar, R., Wilson, G.V., Provart, N.J., 2007. An “Electronic Fluorescent Pictograph” browser for exploring and analyzing large-scale biological data sets. PloS one 2, e718.