Table S4.4. Cluster 4 markers  identified in the first single-cell 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 　 　
LOC107438948 3.25E-30 1.05253958 0.559 0.09 5.75E-26 LOC107438948 rhomboid-related protein 2 aug3.g13481 Pt-rhomboid-A hh5 - ptc5 - msx6 +    
LOC107437911 2.81E-27 1.25690612 0.898 0.419 4.96E-23 LOC107437911 serine protease 27 aug3.g12644 (serine protease) hh5 + ptc5 -      
LOC107448645 1.02E-26 1.1357564 0.78 0.256 1.79E-22 LOC107448645 transcription factor Sp9, transcript variant X6 aug3.g2333 Pt-sp hh5 - ptc5 -      
LOC107438714 3.12E-22 1.00277908 0.924 0.607 5.52E-18 LOC107438714 transcriptional activator cubitus interruptus-like, transcript variant X1 aug3.g13321 Pt-ci hh5 + ptc5 -      
LOC107456088 1.30E-18 0.85950955 0.492 0.121 2.30E-14 LOC107456088 iroquois-class homeodomain protein IRX-6, transcript variant X1 aug3.g8295 Pt-mirr4 hh5 - ptc5 - msx6 + fuchi3 +  
LOC107450100 2.94E-18 0.83790171 0.678 0.253 5.19E-14 LOC107450100 homeobox protein DLX-6-like, transcript variant X1 aug3.g15531 Pt-dll   ptc5 -      
LOC107442769 4.38E-18 0.78019943 0.992 0.778 7.74E-14 LOC107442769 neurogenic locus Notch protein aug3.g27737 　          
LOC107454167 6.25E-18 0.69141045 0.576 0.173 1.10E-13 LOC107454167 dorsal-ventral patterning protein Sog-like aug3.g23966 Pt-sog   ptc5 -   fuchi3 +  
LOC107444558 9.40E-16 0.68335626 0.517 0.16 1.66E-11 LOC107444558 paired box protein Pax-5, transcript variant X1 aug3.g762 　   ptc5 -      
LOC107446842 1.86E-14 0.71343985 0.975 0.718 3.28E-10 LOC107446842 uncharacterized LOC107446842 aug3.g1486 　 hh5 -     fuchi3 +  
LOC107450033 1.36E-13 0.65295845 0.847 0.543 2.41E-09 LOC107450033 protein pangolin, isoforms A/H/I/S, transcript variant X3 aug3.g10490 　          
LOC107447678 2.59E-13 0.59410512 0.568 0.204 4.57E-09 LOC107447678 homeobox protein MSH-D-like aug3.g15189 Pt-msx1 hh5 + ptc5 -      
LOC107448055 1.96E-12 1.16789501 0.542 0.235 3.47E-08 LOC107448055 uncharacterized LOC107448055, transcript variant X1 aug3.g2047 　       fuchi3 - fuchi5 -
LOC107438732 5.57E-10 0.54394306 0.805 0.488 9.84E-06 LOC107438732 somatomedin-B and thrombospondin type-1 domain-containing protein-like aug3.g26535 　   ptc5 -      
LOC107457539 1.02E-09 0.61874727 0.797 0.53 1.80E-05 LOC107457539 zinc finger homeobox protein 3-like, transcript variant X2 aug3.g11268 　 hh5 -     fuchi3 +  
LOC107447950 1.42E-09 0.53545123 0.992 0.948 2.51E-05 LOC107447950 protein lifeguard 2-like, transcript variant X1 aug3.g15222 　 hh5 +        
LOC107452584 1.51E-09 0.59718295 0.661 0.364 2.67E-05 LOC107452584 secreted frizzled-related protein 5 aug3.g4876 Pt-Secreted frizzled-related protein hh5 - ptc5 -      
LOC107441771 1.06E-07 0.54444861 0.72 0.468 1.87E-03 LOC107441771 protein tiptop-like, transcript variant X1 aug3.g25516 　       fuchi3 +  
LOC107442927 1.36E-07 0.37594544 0.703 0.421 2.40E-03 LOC107442927 　 　 　 　 　 　 　 　
LOC107436691 1.81E-07 0.51282255 0.619 0.333 3.20E-03 LOC107436691 uncharacterized LOC107436691, transcript variant X2 aug3.g11765 　 hh5 - ptc5 -      
LOC107453655 1.93E-07 0.40149337 0.992 0.93 3.42E-03 LOC107453655 RNA-binding protein MEX3B-like aug3.g5665 　          
*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