Adam, M., Potter, A.S., Potter, S.S., 2017. Psychrophilic proteases dramatically reduce single-cell
RNA-seq artifacts: A molecular atlas of kidney development. Dev. Camb. 144, 3625–3632.
https://doi.org/10.1242/dev.151142
Aibar, S., González-Blas, C.B., Moerman, T., Huynh-Thu, V.A., Imrichova, H., Hulselmans, G.,
Rambow, F., Marine, J.C., Geurts, P., Aerts, J., Van Den Oord, J., Atak, Z.K., Wouters, J., Aerts, S.,
2017. SCENIC: Single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–
1086. https://doi.org/10.1038/nmeth.4463
Alberga, A., Boulay, J.L., Kempe, E., Dennefeld, C., Haenlin, M., 1991. The snail gene required
for mesoderm formation in Drosophila is expressed dynamically in derivatives of all three germ
layers. Development 111, 983–992. https://doi.org/10.1242/dev.111.4.983
Albright, A.R., Stadler, M.R., Eisen, M.B., 2022. Single-nucleus RNA-sequencing in precellularization Drosophila melanogaster embryos. PLoS ONE 17, 1–13.
https://doi.org/10.1371/journal.pone.0270471
Ashton, J.M., Rehrauer, H., Myers, Jason, Myers, Jacqueline, Zanche, M., Balys, M., Foox, J.,
Mason, C.E., Steen, R., Kuentzel, M., Aquino, C., Garcia-Reyero, N., Chittur, S.V., 2021.
Comparative Analysis of Single-Cell RNA Sequencing Platforms and Methods. J. Biomol. Tech.
JBT 32, 3fc1f5fe.3eccea01. https://doi.org/10.7171/3fc1f5fe.3eccea01
Bailles, A., Collinet, C., Philippe, J.-M., Lenne, P.-F., Munro, E., Lecuit, T., 2019. Genetic
induction and mechanochemical propagation of a morphogenetic wave. Nature 572, 467–473.
https://doi.org/10.1038/s41586-019-1492-9
Bakken, T.E., Hodge, R.D., Miller, J.A., Yao, Z., Nguyen, T.N., Aevermann, B., Barkan, E.,
Bertagnolli, D., Casper, T., Dee, N., Garren, E., Goldy, J., Graybuck, L.T., Kroll, M., Lasken, R.S.,
Lathia, K., Parry, S., Rimorin, C., Scheuermann, R.H., Schork, N.J., Shehata, S.I., Tieu, M., Phillips,
J.W., Bernard, A., Smith, K.A., Zeng, H., Lein, E.S., Tasic, B., 2018. Single-nucleus and single-cell
transcriptomes compared in matched cortical cell types. PLOS ONE 13, e0209648.
https://doi.org/10.1371/journal.pone.0209648
Basile, G., Kahraman, S., Dirice, E., Pan, H., Dreyfuss, J.M., Kulkarni, R.N., 2021. Using singlenucleus RNA-sequencing to interrogate transcriptomic profiles of archived human pancreatic islets.
Genome Med. 13, 128. https://doi.org/10.1186/s13073-021-00941-8
Beliveau, B.J., Kishi, J.Y., Nir, G., Sasaki, H.M., Saka, S.K., Nguyen, S.C., Wu, C.-T., Yin, P.,
2018. OligoMiner provides a rapid, flexible environment for the design of genome-scale
143
oligonucleotide in situ hybridization probes. Proc. Natl. Acad. Sci. U. S. A. 115, E2183–E2192.
https://doi.org/10.1073/pnas.1714530115
Berleth, T., Burri, M., Thoma, G., Bopp, D., Richstein, S., Frigerio, G., Noll, M., NüssleinVolhard, C., 1988. The role of localization of bicoid RNA in organizing the anterior pattern of the
Drosophila embryo. EMBO J. 7, 1749–1756. https://doi.org/10.1002/j.1460-2075.1988.tb03004.x
Bertet, C., Sulak, L., Lecuit, T., 2004. Myosin-dependent junction remodelling controls planar cell
intercalation and axis elongation. Nature. https://doi.org/10.1038/nature02590
Briggs, J.A., Weinreb, C., Wagner, D.E., Megason, S., Peshkin, L., Kirschner, M.W., Klein, A.M.,
2018. The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution.
Science 360. https://doi.org/10.1126/science.aar5780
Briscoe, J., Small, S., 2015. Morphogen rules: Design principles of gradient-mediated embryo
patterning. Dev. Camb. 142, 3996–4009. https://doi.org/10.1242/dev.129452
Calderon, D., Blecher-Gonen, R., Huang, X., Secchia, S., Kentro, J., Daza, R.M., Martin, B.,
Dulja, A., Schaub, C., Trapnell, C., Larschan, E., O’Connor-Giles, K.M., Furlong, E.E.M., Shendure,
J., 2022. The continuum of Drosophila embryonic development at single-cell resolution. Science
377, 1–40. https://doi.org/10.1126/science.abn5800
Cammarota, C., Finegan, T.M., Wilson, T.J., Yang, S., Bergstralh, D.T., 2020. An AxonPathfinding Mechanism Preserves Epithelial Tissue Integrity. Curr. Biol. CB 30, 5049-5057.e3.
https://doi.org/10.1016/j.cub.2020.09.061
Casanova, J., Struhl, G., 1989. Localized surface activity of torso, a receptor tyrosine kinase,
specifies terminal body pattern in Drosophila. Genes Dev. 3, 2025–2038.
https://doi.org/10.1101/gad.3.12b.2025
Chen, S., Mar, J.C., 2018. Evaluating methods of inferring gene regulatory networks highlights
their lack of performance for single cell gene expression data. BMC Bioinformatics 19, 232.
https://doi.org/10.1186/s12859-018-2217-z
Chen, S., Zhou, Y., Chen, Y., Gu, J., 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor.
Bioinforma. Oxf. Engl. 34, i884–i890. https://doi.org/10.1093/bioinformatics/bty560
Clark, E., Akam, M., 2016. Odd-paired controls frequency doubling in Drosophila segmentation
by altering the pair-rule gene regulatory network. eLife 5, 1–42. https://doi.org/10.7554/eLife.18215
Cowden, J., Levine, M., 2002. The Snail repressor positions Notch signaling in the Drosophila
embryo. Development 129, 1785–1793. https://doi.org/10.1242/dev.129.7.1785
Del Álamo, D., Rouault, H., Schweisguth, F., 2011. Mechanism and significance of cis-inhibition
in notch signalling. Curr. Biol. 21, 40–47. https://doi.org/10.1016/j.cub.2010.10.034
144
Ding, X.B., Jin, J., Tao, Y.T., Guo, W.P., Ruan, L., Yang, Q.L., Chen, P.C., Yao, H., Zhang, H.B.,
Chen, X., 2020. Predicted Drosophila Interactome Resource and web tool for functional
interpretation of differentially expressed genes. Database J. Biol. Databases Curation 2020, 1–11.
https://doi.org/10.1093/database/baaa005
Driever, W., Nüsslein-Volhard, C., 1988. The bicoid protein determines position in the Drosophila
embryo in a concentration-dependent manner. Cell 54, 95–104.
Farrell, J.A., Wang, Y., Riesenfeld, S.J., Shekhar, K., Regev, A., Schier, A.F., 2018. Single-cell
reconstruction of developmental trajectories during zebrafish embryogenesis. Science 360.
https://doi.org/10.1126/science.aar3131
Finak, G., McDavid, A., Yajima, M., Deng, J., Gersuk, V., Shalek, A.K., Slichter, C.K., Miller,
H.W., McElrath, M.J., Prlic, M., Linsley, P.S., Gottardo, R., 2015. MAST: a flexible statistical
framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA
sequencing data. Genome Biol. 16, 278. https://doi.org/10.1186/s13059-015-0844-5
Finklstein, R., Perrimon, N., 1990. The orthodenticle gene is regulated by bicoid and torso and
specifies Drosophila head development. Nature 346, 485–488. https://doi.org/10.1038/346485a0
Fowlkes, C.C., Hendriks, C.L.L., Keränen, S.V.E., Weber, G.H., Rübel, O., Huang, M.-Y.,
Chatoor, S., DePace, A.H., Simirenko, L., Henriquez, C., Beaton, A., Weiszmann, R., Celniker, S.,
Hamann, B., Knowles, D.W., Biggin, M.D., Eisen, M.B., Malik, J., 2008. A Quantitative
Spatiotemporal Atlas of Gene Expression in the Drosophila Blastoderm. Cell 133, 364–374.
https://doi.org/10.1016/j.cell.2008.01.053
Frohnhöfer, H.G., Nüsslein-Volhard, C., 1986. Organization of anterior pattern in the Drosophila
embryo by the maternal gene bicoid. Nature 324, 120–125. https://doi.org/10.1038/324120a0
Ganguly, A., Jiang, J., Ip, Y.T., 2005. Drosophila WntD is a target and an inhibitor of the Dorsal /
Twist / Snail network in the gastrulating embryo 3419–3429. https://doi.org/10.1242/dev.01903
Gavis, E.R., Lehmann, R., 1992. Localization of nanos RNA controls embryonic polarity. Cell 71,
301–313. https://doi.org/10.1016/0092-8674(92)90358-J
Gilmour, D., Rembold, M., Leptin, M., 2017. From morphogen to morphogenesis and back.
Nature 541, 311–320. https://doi.org/10.1038/nature21348
Graham, P.L., Anderson, W.R., Brandt, E.A., Xiang, J., Pick, L., 2019. Dynamic expression of
Drosophila segmental cell surface-encoding genes and their pair-rule regulators. Dev. Biol. 447,
147–156. https://doi.org/10.1016/j.ydbio.2019.01.015
Hammonds, A.S., Bristow, C.A., Fisher, W.W., Weiszmann, R., Wu, S., Hartenstein, V., Kellis,
M., Yu, B., Frise, E., Celniker, S.E., 2013. Spatial expression of transcription factors in Drosophila
145
embryonic organ development. Genome Biol. 14, R140. https://doi.org/10.1186/gb-2013-14-12-r140
Heemskerk, J., DiNardo, S., 1994. Drosophila hedgehog acts as a morphogen in cellular
patterning. Cell 76, 449–460. https://doi.org/10.1016/0092-8674(94)90110-4
Heimberg, G., Bhatnagar, R., El-Samad, H., Thomson, M., 2016. Low Dimensionality in Gene
Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow
Sequencing. Cell Syst. 2, 239–250. https://doi.org/10.1016/j.cels.2016.04.001
Hinck, L., 2004. The versatile roles of “axon guidance” cues in tissue morphogenesis. Dev. Cell 7,
783–93. https://doi.org/10.1016/j.devcel.2004.11.002
Hu, Y., Comjean, A., Perkins, L.A., Perrimon, N., Mohr, S.E., 2015. GLAD: an Online Database
of G ene L ist A nnotation for D rosophila. J. Genomics 3, 75–81. https://doi.org/10.7150/jgen.12863
Hunter, J.D., 2007. Matplotlib: A 2D Graphics Environment. Comput. Sci. Eng. 9, 90–95.
https://doi.org/10.1109/MCSE.2007.55
Ingham, P.W., Arias, A.M., 1992. Boundaries and fields in early embryos. Cell 68, 221–235.
https://doi.org/10.1016/0092-8674(92)90467-Q
Irvine, K.D., Wieschaus, E., 1994. Cell intercalation during Drosophila germband extension and
its regulation by pair-rule segmentation genes. Development 120, 827–841.
Islam, S., Zeisel, A., Joost, S., Manno, G.L., Zajac, P., Kasper, M., Lönnerberg, P., Linnarsson, S.,
2014. Quantitative single-cell RNA-seq with unique molecular identifiers 11.
https://doi.org/10.1038/nmeth.2772
Jack, T., McGinnis, W., 1990. Establishment of the Deformed expression stripe requires the
combinatorial action of coordinate, gap and pair-rule proteins. EMBO J. 9, 1187–1198.
https://doi.org/10.1002/j.1460-2075.1990.tb08226.x
Janssens, J., Aibar, S., Taskiran, I.I., Ismail, J.N., Gomez, A.E., Aughey, G., Spanier, K.I., De
Rop, F.V., González-Blas, C.B., Dionne, M., Grimes, K., Quan, X.J., Papasokrati, D., Hulselmans,
G., Makhzami, S., De Waegeneer, M., Christiaens, V., Southall, T., Aerts, S., 2022. Decoding gene
regulation in the fly brain. Nature 601, 630–636. https://doi.org/10.1038/s41586-021-04262-z
Kaminow, B., Yunusov, D., Dobin, A., Spring, C., 2021. STARsolo : accurate , fast and versatile
mapping / quantification of single-cell and single-nucleus RNA-seq data 1–35.
Karaiskos, N., Wahle, P., Alles, J., Boltengagen, A., Ayoub, S., Kipar, C., Kocks, C., Rajewsky,
N., Zinzen, R.P., 2017. The Drosophila embryo at single-cell transcriptome resolution. Science 358,
194–199. https://doi.org/10.1126/science.aan3235
Keleman, K., Rajagopalan, S., Cleppien, D., Teis, D., Paiha, K., Huber, L.A., Technau, G.M.,
Dickson, B.J., 2002. Comm sorts robo to control axon guidance at the Drosophila midline. Cell 110,
146
415–27. https://doi.org/10.1016/s0092-8674(02)00901-7
Keleman, K., Ribeiro, C., Dickson, B.J., 2005. Comm function in commissural axon guidance:
cell-autonomous sorting of Robo in vivo. Nat. Neurosci. 8, 156–63. https://doi.org/10.1038/nn1388
Kishi, J.Y., Lapan, S.W., Beliveau, B.J., West, E.R., Zhu, A., Sasaki, H.M., Saka, S.K., Wang, Y.,
Cepko, C.L., Yin, P., 2019. SABER amplifies FISH: enhanced multiplexed imaging of RNA and
DNA in cells and tissues. Nat. Methods 16, 533–544. https://doi.org/10.1038/s41592-019-0404-0
Kolodziejczyk, A.A., Kim, J.K., Svensson, V., Marioni, J.C., Teichmann, S.A., 2015. The
Technology and Biology of Single-Cell RNA Sequencing. Mol. Cell 58, 610–620.
https://doi.org/10.1016/j.molcel.2015.04.005
Kondo, T., Hayashi, S., 2019. Two-step regulation of trachealess ensures tight coupling of cell fate
with morphogenesis in the drosophila trachea. eLife 8, 1–23. https://doi.org/10.7554/eLife.45145
Korsunsky, I., Millard, N., Fan, J., Slowikowski, K., Zhang, F., Wei, K., Baglaenko, Y., Brenner,
M., Loh, P. ru, Raychaudhuri, S., 2019. Fast, sensitive and accurate integration of single-cell data
with Harmony. Nat. Methods 16, 1289–1296. https://doi.org/10.1038/s41592-019-0619-0
Krueger, D., Tardivo, P., Nguyen, C., De Renzis, S., 2018. Downregulation of basal myosin‐II is
required for cell shape changes and tissue invagination. EMBO J. 37, 1–16.
https://doi.org/10.15252/embj.2018100170
Leptin, M., Grunewald, B., 1990. Cell shape changes during gastrulation in Drosophila.
Development 110, 73–84.
Letsou, W., Cai, L., 2016. Noncommutative Biology: Sequential Regulation of Complex
Networks. PLOS Comput. Biol. 12, e1005089. https://doi.org/10.1371/journal.pcbi.1005089
Li, B., Dewey, C.N., 2011. RSEM: accurate transcript quantification from RNA-Seq data with or
without a reference genome. BMC Bioinformatics 12, 323. https://doi.org/10.1186/1471-2105-12323
Liu, W., Morgan, K.M., Pine, S.R., 2014. Activation of the Notch1 Stem Cell Signaling Pathway
during Routine Cell Line Subculture. Front. Oncol. 4, 1–4. https://doi.org/10.3389/fonc.2014.00211
Long, H.K., Prescott, S.L., Wysocka, J., 2016. Ever-Changing Landscapes: Transcriptional
Enhancers in Development and Evolution. Cell 167, 1170–1187.
https://doi.org/10.1016/j.cell.2016.09.018
Luengo Hendriks, C.L., Keränen, S.V.E., Fowlkes, C.C., Simirenko, L., Weber, G.H., DePace,
A.H., Henriquez, C., Kaszuba, D.W., Hamann, B., Eisen, M.B., Malik, J., Sudar, D., Biggin, M.D.,
Knowles, D.W., 2006. Three-dimensional morphology and gene expression in the Drosophila
blastoderm at cellular resolution I: Data acquisition pipeline. Genome Biol. 7.
147
https://doi.org/10.1186/gb-2006-7-12-r123
Macosko, E.Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas,
A.R., Kamitaki, N., Martersteck, E.M., Trombetta, J.J., Weitz, D.A., Sanes, J.R., Shalek, A.K.,
Regev, A., McCarroll, S.A., 2015. Highly Parallel Genome-wide Expression Profiling of Individual
Cells Using Nanoliter Droplets. Cell 161, 1202–1214. https://doi.org/10.1016/j.cell.2015.05.002
Manning, A.J., Peters, K.A., Peifer, M., Rogers, S.L., 2013. Regulation of Epithelial
Morphogenesis by the G Protein–Coupled Receptor Mist and Its Ligand Fog. Sci. Signal. 6, 1–11.
https://doi.org/10.1126/scisignal.2004427
Martin, A.C., Kaschube, M., Wieschaus, E.F., 2009. Pulsed contractions of an actin–myosin
network drive apical constriction. Nature 457, 495–499. https://doi.org/10.1038/nature07522
Martin, M., 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads.
EMBnet.journal 17, 10. https://doi.org/10.14806/ej.17.1.200
Martinez-Arias, A., Lawrence, P.A., 1985. Parasegments and compartments in the Drosophila
embryo. Nature 313, 639–642. https://doi.org/10.1038/313639a0
Morel, V., Schweisguth, F., 2000. Repression by suppressor of hairless and activation by Notch
are required to define a single row of single-minded expressing cells in the Drosophila embryo.
Genes Dev. 14, 377–88.
Moriel, N., Senel, E., Friedman, N., Rajewsky, N., Karaiskos, N., Nitzan, M., 2021. NovoSpaRc:
flexible spatial reconstruction of single-cell gene expression with optimal transport. Nat. Protoc. 16,
4177–4200. https://doi.org/10.1038/s41596-021-00573-7
Nüsslein-Volhard, C., Wieschaus, E., 1980. Mutations affecting segment number and polarity in
Drosophila. Nature 287, 795–801. https://doi.org/10.1038/287795a0
O’Flanagan, C.H., Campbell, K.R., Zhang, A.W., Kabeer, F., Lim, J.L.P., Biele, J., Eirew, P., Lai,
D., McPherson, A., Kong, E., Bates, C., Borkowski, K., Wiens, M., Hewitson, B., Hopkins, J., Pham,
J., Ceglia, N., Moore, R., Mungall, A.J., McAlpine, J.N., Shah, S.P., Aparicio, S., 2019. Dissociation
of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved
collagenase-associated stress responses. Genome Biol. 20, 210. https://doi.org/10.1186/s13059-0191830-0
Okochi, Y., Sakaguchi, S., Nakae, K., Kondo, T., Naoki, H., 2021. Model-based prediction of
spatial gene expression via generative linear mapping. Nat. Commun. 12, 1–13.
https://doi.org/10.1038/s41467-021-24014-x
Packer, J.S., Zhu, Q., Huynh, C., Sivaramakrishnan, P., Preston, E., Dueck, H., Stefanik, D., Tan,
K., Trapnell, C., Kim, J., Waterston, R.H., Murray, J.I., 2019. A lineage-resolved molecular atlas of
148
C. elegans embryogenesis at single-cell resolution. Science 365.
https://doi.org/10.1126/science.aax1971
Paré, A.C., Naik, P., Shi, J., Mirman, Z., Palmquist, K.H., Zallen, J.A., 2019. An LRR ReceptorTeneurin System Directs Planar Polarity at Compartment Boundaries. Dev. Cell 51, 208-221.e6.
https://doi.org/10.1016/j.devcel.2019.08.003
Paré, A.C., Vichas, A., Fincher, C.T., Mirman, Z., Farrell, D.L., Mainieri, A., Zallen, J.A., 2014.
A positional Toll receptor code directs convergent extension in Drosophila. Nature 515, 523–527.
https://doi.org/10.1038/nature13953
Paroush, Z., Mark Wainwright, S., Ish-Horowicz, D., 1997. Torso signalling regulates terminal
patterning in Drosophila by antagonising Groucho-mediated repression. Development 124, 3827–
3834.
Petkova, M.D., Tkačik, G., Bialek, W., Wieschaus, E.F., Gregor, T., 2019. Optimal Decoding of
Cellular Identities in a Genetic Network. Cell 176, 844-855.e15.
https://doi.org/10.1016/j.cell.2019.01.007
Rahimi, N., Averbukh, I., Haskel-Ittah, M., Degani, N., Schejter, E.D., Barkai, N., Shilo, B.-Z.,
2016. A WntD-Dependent Integral Feedback Loop Attenuates Variability in Drosophila Toll
Signaling. Dev. Cell 36, 401–414. https://doi.org/10.1016/j.devcel.2016.01.023
Rauzi, M., Lenne, P.-F., Lecuit, T., 2010. Planar polarized actomyosin contractile flows control
epithelial junction remodelling. Nature 468, 1110–1114. https://doi.org/10.1038/nature09566
Reeves, G.T., Stathopoulos, A., 2009. Graded Dorsal and Differential Gene Regulation in the
Drosophila Embryo. Cold Spring Harb. Perspect. Biol. 1, a000836–a000836.
https://doi.org/10.1101/cshperspect.a000836
Reuter, R., Grunewald, B., Leptin, M., 1993. A role for the mesoderm in endodermal migration
and morphogenesis in Drosophila. Dev. Camb. Engl. 119, 1135–45.
https://doi.org/10.1242/dev.119.4.1135
Robinson, M.D., McCarthy, D.J., Smyth, G.K., 2010. edgeR: a Bioconductor package for
differential expression analysis of digital gene expression data. Bioinforma. Oxf. Engl. 26, 139–40.
https://doi.org/10.1093/bioinformatics/btp616
Satija, R., Farrell, J.A., Gennert, D., Schier, A.F., Regev, A., 2015. Spatial reconstruction of
single-cell gene expression data. Nat. Biotechnol. 33, 495–502. https://doi.org/10.1038/nbt.3192
Schaerlinger, B., Launay, J.M., Vonesch, J.I., Maroteaux, L., 2007. Gain of affinity point mutation
in the serotonin receptor gene 5-HT 2Dro accelerates germband extension movements during
Drosophila gastrulation. Dev. Dyn. 236, 991–999. https://doi.org/10.1002/dvdy.21110
149
Staller, M.V., Fowlkes, C.C., Bragdon, M.D.J., Wunderlich, Z., Estrada, J., DePace, A.H., 2015. A
gene expression atlas of a bicoid -depleted Drosophila embryo reveals early canalization of cell fate.
Development 142, 587–596. https://doi.org/10.1242/dev.117796
Stedden, C.G., Menegas, W., Zajac, A.L., Williams, A.M., Cheng, S., Özkan, E., HorneBadovinac, S., 2019. Planar-Polarized Semaphorin-5c and Plexin A Promote the Collective
Migration of Epithelial Cells in Drosophila. Curr. Biol. CB 29, 908-920.e6.
https://doi.org/10.1016/j.cub.2019.01.049
Stern, T., Shvartsman, S.Y., Wieschaus, E.F., 2022. Deconstructing gastrulation at single-cell
resolution. Curr. Biol. CB 32, 1861–1868. https://doi.org/10.1016/j.cub.2022.02.059
Stricker, S.H., Köferle, A., Beck, S., 2016. From profiles to function in epigenomics. Nat. Rev.
Genet. 18, 51–66. https://doi.org/10.1038/nrg.2016.138
Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W.M., Hao, Y.,
Stoeckius, M., Smibert, P., Satija, R., 2019. Comprehensive Integration of Single-Cell Data. Cell
177, 1888-1902.e21. https://doi.org/10.1016/j.cell.2019.05.031
Sweeton, D., Parks, S., Costa, M., Wieschaus, E., 1991. Gastrulation in Drosophila: The formation
of the ventral furrow and posterior midgut invaginations. Development 112, 775–789.
Tanay, A., Regev, A., 2017. Scaling single-cell genomics from phenomenology to mechanism.
Nature 541, 331–338. https://doi.org/10.1038/nature21350
Tetley, R.J., Blanchard, G.B., Fletcher, A.G., Adams, R.J., Sanson, B., 2016. Unipolar
distributions of junctional myosin II identify cell stripe boundaries that drive cell intercalation
throughout drosophila axis extension. eLife 5, 1–28. https://doi.org/10.7554/eLife.12094
Thisse, B., Stoetzel, C., Gorostiza-Thisse, C., Perrin-Schmitt, F., 1988. Sequence of the twist gene
and nuclear localization of its protein in endomesodermal cells of early Drosophila embryos. EMBO
J. 7, 2175–2183. https://doi.org/10.1002/j.1460-2075.1988.tb03056.x
Tomancak, P., Beaton, A., Weiszmann, R., Kwan, E., Shu, S., Lewis, S.E., Richards, S.,
Ashburner, M., Hartenstein, V., Celniker, S.E., Rubin, G.M., 2002. Systematic determination of
patterns of gene expression during Drosophila embryogenesis. Genome Biol. 3, RESEARCH0088.
https://doi.org/10.1186/gb-2002-3-12-research0088
Tomancak, P., Berman, B.P., Beaton, A., Weiszmann, R., Kwan, E., Hartenstein, V., Celniker,
S.E., Rubin, G.M., 2007. Global analysis of patterns of gene expression during Drosophila
embryogenesis. Genome Biol. 8, R145. https://doi.org/10.1186/gb-2007-8-7-r145
Vaughen, J., Igaki, T., 2016. Slit-Robo Repulsive Signaling Extrudes Tumorigenic Cells from
Epithelia. Dev. Cell 39, 683–695. https://doi.org/10.1016/j.devcel.2016.11.015
150
Vincent, A., Blankenship, J.T., Wieschaus, E., 1997. Integration of the head and trunk
segmentation systems controls cephalic furrow formation in Drosophila. Development 124, 3747–
3754.
Virtanen, P., Gommers, R., Oliphant, T.E., Haberland, M., Reddy, T., Cournapeau, D., Burovski,
E., Peterson, P., Weckesser, W., Bright, J., van der Walt, S.J., Brett, M., Wilson, J., Millman, K.J.,
Mayorov, N., Nelson, A.R.J., Jones, E., Kern, R., Larson, E., Carey, C.J., Polat, İ., Feng, Y., Moore,
E.W., VanderPlas, J., Laxalde, D., Perktold, J., Cimrman, R., Henriksen, I., Quintero, E.A., Harris,
C.R., Archibald, A.M., Ribeiro, A.H., Pedregosa, F., van Mulbregt, P., Vijaykumar, A., Bardelli,
A.P., Rothberg, A., Hilboll, A., Kloeckner, A., Scopatz, A., Lee, A., Rokem, A., Woods, C.N.,
Fulton, C., Masson, C., Häggström, C., Fitzgerald, C., Nicholson, D.A., Hagen, D.R., Pasechnik,
D.V., Olivetti, E., Martin, E., Wieser, E., Silva, F., Lenders, F., Wilhelm, F., Young, G., Price, G.A.,
Ingold, G.-L., Allen, G.E., Lee, G.R., Audren, H., Probst, I., Dietrich, J.P., Silterra, J., Webber, J.T.,
Slavič, J., Nothman, J., Buchner, J., Kulick, J., Schönberger, J.L., de Miranda Cardoso, J.V., Reimer,
J., Harrington, J., Rodríguez, J.L.C., Nunez-Iglesias, J., Kuczynski, J., Tritz, K., Thoma, M.,
Newville, M., Kümmerer, M., Bolingbroke, M., Tartre, M., Pak, M., Smith, N.J., Nowaczyk, N.,
Shebanov, N., Pavlyk, O., Brodtkorb, P.A., Lee, P., McGibbon, R.T., Feldbauer, R., Lewis, S.,
Tygier, S., Sievert, S., Vigna, S., Peterson, S., More, S., Pudlik, T., Oshima, T., Pingel, T.J.,
Robitaille, T.P., Spura, T., Jones, T.R., Cera, T., Leslie, T., Zito, T., Krauss, T., Upadhyay, U.,
Halchenko, Y.O., Vázquez-Baeza, Y., 2020. SciPy 1.0: fundamental algorithms for scientific
computing in Python. Nat. Methods 17, 261–272. https://doi.org/10.1038/s41592-019-0686-2
Wang, Y.C., Khan, Z., Kaschube, M., Wieschaus, E.F., 2012. Differential positioning of adherens
junctions is associated with initiation of epithelial folding. Nature 484, 390–393.
https://doi.org/10.1038/nature10938
Weigel, D., Jürgens, G., Klingler, M., Jäckle, H., 1990. Two gap genes mediate maternal terminal
pattern information in Drosophila. Science 248, 495–498. https://doi.org/10.1126/science.2158673
Wu, Y.E., Pan, L., Zuo, Y., Li, X., Hong, W., 2017. Detecting Activated Cell Populations Using
Single-Cell RNA-Seq. Neuron 96, 313-329.e6. https://doi.org/10.1016/j.neuron.2017.09.026
Yazdani, U., Terman, J.R., 2006. The semaphorins. Genome Biol. 7, 211.
https://doi.org/10.1186/gb-2006-7-3-211
Yoo, S.K., Pascoe, H.G., Pereira, T., Kondo, S., Jacinto, A., Zhang, X., Hariharan, I.K., 2016.
Plexins function in epithelial repair in both Drosophila and zebrafish. Nat. Commun. 7, 12282.
https://doi.org/10.1038/ncomms12282
Zallen, J.A., Wieschaus, E., 2004. Patterned Gene Expression Directs Bipolar Planar Polarity in
Drosophila. Dev. Cell 6, 343–355.
Zhang, M.J., Ntranos, V., Tse, D., 2020. Determining sequencing depth in a single-cell RNA-seq
151
experiment. Nat. Commun. 11, 774. https://doi.org/10.1038/s41467-020-14482-y
Zinzen, R.P., Cande, J., Ronshaugen, M., Papatsenko, D., Levine, M., 2006. Evolution of the
Ventral Midline in Insect Embryos. Dev. Cell 11, 895–902.
https://doi.org/10.1016/j.devcel.2006.10.012
注釈
本研究は複数の共同研究者とともに行った。本研究において、scRNA-seqデータの取得
は近藤武史博士と共同で行った。また、バルクRNA-seqの実行と解析は近藤武史博士が行
った。加えて、図 24のFISH実験と画像の取得は水野苑子さんが行った。
謝辞
本研究に関して、上村匡教授には私が学部生の頃から非常に熱心な指導をしていただき
ました。ラボセミナーやミーティングでの議論を介して、研究者としての姿勢を学ばせて
いただきました。近藤武史博士には、実験手法、データの取り扱い、文書の作成、研究発
表のしかたなど研究活動を行うにあたって必要な多くの事項を指導していただきました。
また、日々の研究の結果に関して、熱心かつ綿密な議論をしていただき、そのうえで研究
計画について数々の助言をいただきました。碓井理夫博士と坪井有寿博士、春本敏之博士
にはグループミーティングにおいて本研究に関する議論をしていただきました。二股真由
美さん、三木雅代さんには、実験の補助をしていただきました。沖かなえさん、森口良子
さん、今井博子さんには教務関連の補佐をしていただきました。また、他の上村研究室の
メンバーの方々にも多くの有意義な助言をいただきました。以上の上村研究室の皆様の手
助けがなければ、本研究を遂行することはできませんでした。心より感謝申し上げます。
本研究を行うにあたり、上村研究室以外の方々にもお世話になりましたのでお名前を上
げさせていただきます。本研究で用いた空間再構成手法 Perler は広島大学の本田直樹教授
と京都大学医学部附属病院の大河内康史医師との共同研究によるものであり、今回の適用
152
に関しても議論と助言をしていただきました。理化学研究所生命機能科学研究センターの
種子島千春さん、西村理さん、門田満隆さんには scRNA-seq 手法の開発の手助けをしてい
ただきました。井垣研究室の山銅ゆかりさんには、qPCR によるライブラリの定量方法、次
世代シーケンサーの使用法に関して指導をしていただきました。Fluidigm 社の甲斐渉さん
には、C1HT のプライマー設計について助言をいただきました。理化学研究所生命機能科学
研究センターの Yu-Chiun Wang 博士にも本研究に関して助言をいただきました。皆様に厚
くお礼申し上げます。 また、本研究は 2020 年 4 月から 2023 年 3 月までの期間、日本学術振興会の特別研究員
DC1 としての支援を受けて行いました。 最後に、支えてくださった家族や友人にも感謝の言葉を述べさせていただきます。本当
にありがとうございました。 本学位論文は以下の学術論文の内容に基づいて書かれたものです。
Shunta Sakaguchi, Sonoko Mizuno, Yasushi Okochi, Chiharu Tanegashima, Osamu Nishimura,
Tadashi Uemura, Mitsutaka Kadota, Honda Naoki and Takefumi Kondo
Single-cell transcriptome atlas of Drosophila gastrula 2.0
Cell Reports, in press, 2023
坂口
153
峻太 ...