Table S9.2. Cluster 9 markers identified in the single-nucleus RNA-seq analysis.
Gene ID (NCBI) p_val avg_log2FC pct.1* pct.2* p_val_adj Gene ID (NCBI) Product (NCBI) aug3 gene model Gene name Expression in RNAi embryos** 　 　
LOC107447499 0 2.78087907 0.742 0.034 0 LOC107447499 uncharacterized LOC107447499 　 　 　 　 　 　 　
LOC107450670 0 1.92144782 0.711 0.029 0 LOC107450670 uncharacterized LOC107450670 aug3.g15599 　   ptc5 - msx6 -    
LOC107452883 4.63E-276 1.59920002 0.535 0.017 9.40E-272 LOC107452883 achaete-scute homolog 1 aug3.g5047 Pt-asl-H   ptc5 - msx6 -    
LOC107453167 5.15E-257 0.97362006 0.403 0.008 1.05E-252 LOC107453167 zinc finger protein 37 aug3.g9318 Pt-krüppel-1 (krü-1)   ptc5 - msx6 -    
LOC107442497 4.96E-220 2.1526487 0.535 0.025 1.01E-215 LOC107442497 uncharacterized LOC107442497 aug3.g27670,aug3.g20943 　 hh5 + ptc5 - msx6 - fuchi3 -  
LOC107451660 1.70E-169 2.4587318 0.654 0.061 3.45E-165 LOC107451660 vitamin K-dependent protein C aug3.g4198 　   ptc5 - msx6 -    
LOC107457039 1.52E-152 1.33670414 0.377 0.018 3.09E-148 LOC107457039 homeobox protein Hox-A9b aug3.g25355 Pt-AbdB-B          
LOC107455285 2.96E-151 2.40091082 0.893 0.156 6.01E-147 LOC107455285 abhydrolase domain-containing protein C22H12.03 aug3.g6972 　   ptc5 -      
LOC107451065 3.07E-117 0.50635515 0.226 0.007 6.24E-113 LOC107451065 uncharacterized LOC107451065 aug3.g3755 　   ptc5 - msx6 -    
LOC107445228 1.12E-113 2.41592585 0.962 0.244 2.28E-109 LOC107445228 protein gooseberry aug3.g18397 Pt-prd2   ptc5 - msx6 -    
LOC107456506 5.79E-107 2.66944678 0.849 0.211 1.18E-102 LOC107456506 uncharacterized LOC107456506 aug3.g8629 　 hh5 +        
LOC122269180 3.33E-86 0.44871323 0.151 0.004 6.77E-82 LOC122269180 uncharacterized LOC122269180 aug3.g15598 　          
LOC107444955 9.47E-74 2.41171727 0.83 0.291 1.93E-69 LOC107444955 uncharacterized LOC107444955 aug3.g887,aug3.g886 　       fuchi3 -  
LOC107451685 1.26E-71 1.91835058 1 0.551 2.55E-67 LOC107451685 roundabout homolog 3 aug3.g10604 Pt-echinoid hh5 + ptc5 -      
LOC107444253 4.91E-66 1.62801809 0.736 0.206 9.97E-62 LOC107444253 transcription factor HES-1-A aug3.g17723 　   ptc5 -      
LOC107453612 1.09E-58 1.310355 0.855 0.279 2.22E-54 LOC107453612 protein Wnt-8b-like aug3.g5617 Pt-wnt8   ptc5 -     fuchi5 -
LOC107452006 4.62E-55 1.79917166 0.893 0.42 9.39E-51 LOC107452006 transcription factor AP-2-beta aug3.g23531 Pt-AP2-A hh5 + ptc5 -      
LOC107438301 4.29E-53 1.93588739 0.805 0.344 8.71E-49 LOC107438301 zinc finger protein 236 aug3.g12961 Pt-zfp236 hh5 + ptc5 -      
LOC107451332 9.09E-49 1.81171552 0.623 0.187 1.85E-44 LOC107451332 uncharacterized LOC107451332 aug3.g3963,aug3.g15729 Pt-ets21c   ptc5 - msx6 +    
LOC107444844 1.69E-47 1.61523003 0.535 0.139 3.42E-43 LOC107444844 protein giant-lens aug3.g839 　   ptc5 -     fuchi5 -
LOC107448951 1.63E-45 1.08088413 0.403 0.081 3.31E-41 LOC107448951 BTB/POZ domain-containing protein kctd15-like aug3.g2480 　 hh5 +       fuchi5 +
LOC107454354 3.44E-44 1.44067937 0.667 0.242 6.99E-40 LOC107454354 semaphorin-5A aug3.g6222 　 hh5 -        
LOC107447180 2.96E-41 1.3844435 0.893 0.406 6.01E-37 LOC107447180 protein Wnt-5b-like aug3.g1632 Pt-wnt5   ptc5 -      
LOC107450899 1.53E-40 1.38542007 0.981 0.603 3.10E-36 LOC107450899 sal-like protein 1 aug3.g3675 　   ptc5 - msx6 -   fuchi5 -
LOC107456184 2.79E-40 0.38517381 0.132 0.009 5.67E-36 LOC107456184 chymotrypsinogen B aug3.g8351 　          
LOC107443647 1.66E-39 1.25874857 0.925 0.484 3.37E-35 LOC107443647 plexin-B aug3.g17369 　         fuchi5 -
LOC107456521 1.68E-37 1.28768993 0.962 0.673 3.40E-33 LOC107456521 ephrin-B2a aug3.g25262 　   ptc5 -      
LOC107441406 7.52E-35 1.61029185 0.786 0.431 1.53E-30 LOC107441406 uncharacterized LOC107441406 aug3.g27275 　 hh5 +        
LOC107438758 5.67E-32 1.0242169 0.987 0.887 1.15E-27 LOC107438758 epidermal growth factor receptor aug3.g13345,aug3.g13344 　          
LOC107450465 2.23E-30 0.90746411 0.692 0.308 4.53E-26 LOC107450465 recombining binding protein suppressor of hairless aug3.g15584 Pt-supressor of hairless          
LOC107441660 5.62E-30 1.23687436 0.937 0.679 1.14E-25 LOC107441660 unconventional myosin-Ie aug3.g9845,aug3.g9846,aug3.g22123            
LOC107442485 1.20E-29 1.18204471 0.855 0.527 2.43E-25 LOC107442485 partitioning defective 3 homolog aug3.g27669 　          
LOC107446742 2.38E-27 0.52817158 0.233 0.043 4.84E-23 LOC107446742 gamma-interferon-inducible lysosomal thiol reductase aug3.g25649 　          
LOC107454244 1.04E-26 0.77710207 1 0.953 2.11E-22 LOC107454244 axin-1 aug3.g6117 Pt-axin          
LOC107438015 1.51E-26 0.79902199 0.384 0.112 3.06E-22 LOC107438015 growth arrest-specific protein 1 aug3.g9575 Pt-gas1 hh5 + ptc5 - msx6 -    
LOC107446080 4.50E-25 1.06602923 0.849 0.519 9.15E-21 LOC107446080 cyclin-dependent kinase 20 aug3.g1238 hh5 +        
LOC107453822 7.04E-25 0.80721808 0.277 0.066 1.43E-20 LOC107453822 midnolin-A aug3.g5791 　          
LOC107451426 2.25E-24 0.84563476 0.384 0.12 4.58E-20 LOC107451426 uncharacterized LOC107451426 aug3.g15724 　          
LOC107439672 1.43E-23 0.80237673 0.811 0.468 2.91E-19 LOC107439672 serine/threonine-protein kinase pim-3 aug3.g13957 　 hh5 -        
LOC107443364 4.29E-23 0.91822861 0.887 0.57 8.71E-19 LOC107443364 uncharacterized LOC107443364 aug3.g17172 　 hh5 +        
LOC107446561 2.46E-22 0.81195126 0.447 0.161 5.00E-18 LOC107446561 small conductance calcium-activated potassium channel protein aug3.g1380,aug3.g23104 　          
LOC107456960 3.31E-22 0.80911254 0.931 0.731 6.72E-18 LOC107456960 suppressor of cytokine signaling 2 aug3.g25340,aug3.g25341 　 hh5 -        
LOC107447307 2.34E-21 0.94800689 0.692 0.348 4.75E-17 LOC107447307 uncharacterized LOC107447307 aug3.g21167 　          
LOC107441688 3.07E-20 0.7262474 0.321 0.096 6.25E-16 LOC107441688 recombining binding protein suppressor of hairless aug3.g27389 　          
LOC107452613 6.78E-20 0.87344702 0.937 0.74 1.38E-15 LOC107452613 lysine-specific demethylase 3B aug3.g292 　          
LOC107436447 2.40E-19 0.35841205 0.189 0.039 4.87E-15 LOC107436447 sex comb on midleg-like protein 4 aug3.g12472,aug3.g11575,aug3.g11576            
LOC107448091 8.09E-19 0.88758266 0.836 0.616 1.64E-14 LOC107448091 rab11 family-interacting protein 4B aug3.g2082,aug3.g22713 　 hh5 +        
LOC107446115 8.84E-19 0.79231548 0.906 0.69 1.80E-14 LOC107446115 extracellular sulfatase Sulf-1 aug3.g18939 　   ptc5 -     fuchi5 +
LOC107454821 1.68E-18 0.65369273 0.377 0.134 3.40E-14 LOC107454821 uncharacterized LOC107454821 aug3.g23640 　          
LOC107440619 2.64E-18 1.04285273 0.912 0.765 5.37E-14 LOC107440619 ETS domain-containing protein Elk-1 aug3.g9766 　          
LOC107448674 5.67E-18 0.91714492 0.836 0.652 1.15E-13 LOC107448674 uncharacterized LOC107448674 aug3.g20402 　          
LOC107443800 1.02E-17 0.2816579 0.145 0.026 2.06E-13 LOC107443800 solute carrier organic anion transporter family member 74D aug3.g532 　          
LOC107438011 1.10E-17 0.50553225 0.516 0.228 2.23E-13 LOC107438011 neurogenic locus protein delta aug3.g12734 Pt-Delta2 hh5 - ptc5 +     fuchi5 -
LOC107450335 1.43E-17 0.87519967 0.572 0.293 2.90E-13 LOC107450335 zinc finger protein basonuclin-2 aug3.g3273 Pt-basonuclin-A hh5 + ptc5 -      
LOC107443537 2.80E-17 0.569094 1 0.942 5.70E-13 LOC107443537 uncharacterized LOC107443537 aug3.g471 　          
LOC107451222 5.41E-17 0.8838206 0.346 0.126 1.10E-12 LOC107451222 uncharacterized LOC107451222 aug3.g21431 　          
LOC107454926 6.92E-17 0.76497009 0.648 0.356 1.41E-12 LOC107454926 bcl-2-like protein 1 aug3.g23010,aug3.g6695,aug3.g6694   hh5 -        
LOC107439278 1.75E-16 0.77998066 0.874 0.697 3.55E-12 LOC107439278 uncharacterized LOC107439278 aug3.g13670 　          
LOC107455560 2.20E-16 0.65304789 0.421 0.175 4.47E-12 LOC107455560 cell division control protein 42 homolog aug3.g7849,aug3.g7850 　          
LOC107448985 3.93E-16 0.65210165 0.604 0.325 7.99E-12 LOC107448985 mucin-12 aug3.g2518 　 hh5 +        
LOC107452888 4.10E-16 0.70158139 0.969 0.831 8.33E-12 LOC107452888 uncharacterized LOC107452888 aug3.g5060 Pt-winged eye-B hh5 + ptc5 -      
LOC107448055 1.04E-15 0.78796089 0.635 0.335 2.12E-11 LOC107448055 pro-epidermal growth factor aug3.g2047 　       fuchi3 - fuchi5 -
LOC107452768 1.21E-15 0.88900497 0.428 0.185 2.46E-11 LOC107452768 cytokine receptor aug3.g4975 　         fuchi5 -
LOC107451864 2.60E-15 0.61888855 0.333 0.12 5.29E-11 LOC107451864 gonadotropin-releasing hormone II receptor aug3.g4360 　          
LOC107451464 3.40E-15 0.65154294 0.704 0.412 6.91E-11 LOC107451464 transcription factor HES-4-A-like aug3.g4026 Pt-hairy   ptc5 -      
LOC107439895 5.21E-15 0.29551319 0.145 0.03 1.06E-10 LOC107439895 cyclin-dependent kinase 4 aug3.g26927 　          
LOC107451223 7.47E-15 0.56775267 0.56 0.291 1.52E-10 LOC107451223 uncharacterized protein DDB_G0271670 aug3.g21432 　          
LOC107447678 1.32E-14 0.64590208 0.409 0.171 2.68E-10 LOC107447678 homeobox protein MSH-D aug3.g15189 Pt-msx1 hh5 + ptc5 -      
LOC107451579 1.06E-13 0.79425107 0.811 0.562 2.15E-09 LOC107451579 E3 ubiquitin-protein ligase Rnf220 aug3.g4121 Pt-rnf220 hh5 - ptc5 -      
LOC107451886 1.08E-13 0.48110546 0.119 0.023 2.20E-09 LOC107451886 hairy/enhancer-of-split related with YRPW motif protein aug3.g4372,aug3.g21564 　          
LOC107457070 1.77E-13 0.73113372 0.686 0.43 3.59E-09 LOC107457070 AP-2 complex subunit alpha-2 aug3.g9061,aug3.g9060 　          
LOC107437786 2.68E-13 0.45336451 0.283 0.1 5.44E-09 LOC107437786 uncharacterized LOC107437786 aug3.g12585 Pt-uninflatable-A hh5 - ptc5 -      
LOC107455742 9.79E-13 0.57418119 0.767 0.535 1.99E-08 LOC107455742 protein hunchback-like aug3.g25126 Pt-hb          
LOC107447162 1.27E-12 0.7736559 0.409 0.199 2.59E-08 LOC107447162 protein C-ets-1 aug3.g19580 　 hh5 -     fuchi3 +  
LOC107447504 4.99E-12 0.60862811 0.459 0.212 1.01E-07 LOC107447504 homeobox protein Hox-B5b aug3.g1787,aug3.g1786 Pt-ftz   ptc5 -      
LOC107455850 7.89E-12 0.74898833 0.667 0.43 1.60E-07 LOC107455850 transmembrane protein 178B aug3.g8086,aug3.g8085 　   ptc5 -      
LOC107447872 7.95E-12 0.4336258 0.22 0.073 1.62E-07 LOC107447872 uncharacterized LOC107447872 aug3.g1960 　   ptc5 -      
LOC107453131 1.19E-11 0.46862264 0.176 0.053 2.42E-07 LOC107453131 alpha-tocopherol transfer protein-like aug3.g5234 　          
LOC107447651 1.63E-11 0.5097005 0.258 0.096 3.32E-07 LOC107447651 uncharacterized LOC107447651 aug3.g1855,aug3.g1854 　          
LOC107453029 1.92E-11 0.37617288 0.176 0.052 3.90E-07 LOC107453029 epidermal growth factor receptor kinase substrate 8 aug3.g5157 　          
LOC107443783 4.60E-11 0.55849773 0.371 0.173 9.34E-07 LOC107443783 plexin-A2 aug3.g428 　          
LOC107447970 9.33E-11 0.46027993 0.943 0.893 1.90E-06 LOC107447970 aurora kinase C aug3.g15230 　 hh5 +        
LOC107457368 1.38E-10 0.29900865 0.195 0.064 2.80E-06 LOC107457368 uncharacterized LOC107457368 aug3.g25891 　          
LOC107445477 1.59E-10 0.61439296 0.698 0.465 3.22E-06 LOC107445477 inaD-like protein aug3.g25607 　   ptc5 +      
LOC110281924 3.49E-10 0.55350955 0.73 0.518 7.09E-06 LOC110281924 triadin aug3.g6466,aug3.g6465 　 hh5 - ptc5 -     fuchi5 +
LOC107453362 4.34E-10 0.69790686 0.667 0.458 8.81E-06 LOC107453362 uncharacterized LOC107453362 aug3.g23776 　          
LOC107456634 1.18E-09 0.584722 0.931 0.851 2.39E-05 LOC107456634 RNA polymerase-associated protein CTR9 homolog aug3.g8712,aug3.g23794 　          
LOC107438220 1.89E-09 0.58016259 0.522 0.317 3.84E-05 LOC107438220 MICAL-like protein 1 aug3.g12909 　 hh5 +        
LOC107457295 2.10E-09 0.50206243 0.591 0.395 4.26E-05 LOC107457295 fructose-bisphosphate aldolase aug3.g11046 　          
LOC107448298 2.82E-09 0.5180911 0.824 0.682 5.73E-05 LOC107448298 transcriptional enhancer factor TEF-1 aug3.g15304 　          
LOC107450046 2.91E-09 0.60197119 0.214 0.082 5.90E-05 LOC107450046 octopamine receptor beta-2R aug3.g3720 　          
LOC107447706 5.68E-09 0.54320942 0.157 0.052 0.0001154 LOC107447706 excitatory amino acid transporter 3 aug3.g1887 　          
LOC107436894 5.99E-09 0.47734118 0.893 0.712 0.00012167 LOC107436894 zinc finger protein rotund aug3.g394 　          
LOC110283330 6.47E-09 0.43098695 0.396 0.206 0.00013145 LOC110283330 uncharacterized LOC110283330 aug3.g21167,aug3.g11138 　          
LOC107441179 7.07E-09 0.49479517 0.943 0.847 0.00014362 LOC107441179 protein grainyhead aug3.g27212,aug3.g23194,aug3.g10582            
LOC107441771 1.25E-08 0.64219559 0.748 0.558 0.00025385 LOC107441771 protein tiptop aug3.g25516 　       fuchi3 +  
LOC107440074 1.50E-08 0.42759681 0.245 0.101 0.00030522 LOC107440074 uncharacterized LOC107440074 aug3.g407 Pt-RTP-B hh5 + ptc5 - msx6 -    
LOC107440250 1.57E-08 0.27681758 0.17 0.06 0.00031859 LOC107440250 uncharacterized LOC107440250 aug3.g20967,aug3.g14385,aug3.g9598     ptc5 -      
LOC107454259 1.95E-08 0.39513244 0.308 0.15 0.00039708 LOC107454259 protocadherin-like wing polarity protein stan aug3.g15160,aug3.g6142,aug3.g22281     ptc5 -      
LOC107445363 3.11E-08 0.53423026 0.138 0.045 0.00063141 LOC107445363 glutathione-specific gamma-glutamylcyclotransferase 1 aug3.g1025 　 hh5 +        
LOC107439384 3.30E-08 0.55387132 0.767 0.562 0.00066951 LOC107439384 ecotropic viral integration site 5 ortholog aug3.g13739 　          
LOC107453601 3.40E-08 0.58308505 0.805 0.659 0.0006913 LOC107453601 protein transport protein Sec24A aug3.g5615 　          
LOC107456664 4.30E-08 0.65004269 0.516 0.332 0.00087427 LOC107456664 uncharacterized LOC107456664 aug3.g8740 　          
*pct1 and pct2 mean proportion of cells that express the gene in this cluster and other clusters, respectively.
**hh5, hh pRNAi at late stage 5; ptc5. ptc pRNAi at late stage 5; msx6, msx1 pRNAi at stage 6;  fuchi3, fuchi pRNAi at stage 3;  fuchi5, fuchi pRNAi at stage 5; +, expression increase; -, expression decrease