SRRs (where applicable) of 164 RNA-seq datasets: 

aboobaker_x1_gfp_072h_01_SRR4068859	
aboobaker_x1_gfp_072h_02_SRR4068860	
aboobaker_x1_lpt_072h_01_SRR4068861 
aboobaker_x1_lpt_072h_02_SRR4068862 
graveley_whole_irra_na_SRR388701 
graveley_whole_na_na_SRR388705 
graveley_x1_na_na_SRR388711 
graveley_x2_na_na_SRR388712
graveley_xins_na_na_SRR388713 
pearson_whole_mex3_288h_SRR2009682 
pearson_whole_mex3_288h_SRR2009683 
pearson_whole_na_168h_SRR2009678 
pearson_whole_na_168h_SRR2009679 
pearson_whole_unc22_288h_SRR2009680 
pearson_whole_unc22_288h_SRR2009681 
pearson_x1_na_na_SRR2009674 
pearson_x1_na_na_SRR2009675 
pearson_x1_na_na_SRR496276 
pearson_x2_na_na_SRR2009676 
pearson_x2_na_na_SRR2009677 
pearson_x2_na_na_SRR496278 
pearson_xins_na_na_SRR496280 
rajewsky_x1_na_na_oenalx1 						       rajewsky_x2_na_na_oenalx2 
rajewsky_xins_na_na_oenalxins 
reddien_prePharyngealX1_anteriorWound_048h_SRR1266970 
reddien_prePharyngealX1_anteriorWound_048h_SRR1266971 
reddien_prePharyngealX1_anteriorWound_048h_SRR1266972 
reddien_prePharyngealX1_na_000h_SRR1266967 
reddien_prePharyngealX1_na_000h_SRR1266968 				   reddien_prePharyngealX1_na_000h_SRR1266969 				reddien_prePharyngealX1_posteriorWound_048h_SRR1266973 			            reddien_prePharyngealX1_posteriorWound_048h_SRR1266974 			         reddien_prePharyngealX1_posteriorWound_048h_SRR1266975 
reddien_x1_na_000h_SRR1302023 
reddien_x1_na_000h_SRR1302024 	
reddien_x1_zfp_120h_SRR1302029 
reddien_x1_zfp_120h_SRR1302030  
reddien_x2_na_000h_SRR1302025 
reddien_x2_na_000h_SRR1302026 
reddien_x2_zfp_120h_SRR1302031 
reddien_x2_zfp_120h_SRR1302032 
sanchez_whole_chd4_072h_SRR2183571 
sanchez_whole_chd4_072h_SRR2183572 
sanchez_whole_chd4_072h_SRR2183573 
sanchez_whole_chd4_144h_SRR2183574 
sanchez_whole_chd4_144h_SRR2183575 
sanchez_whole_chd4_144h_SRR2183576 
sanchez_whole_chd4_216h_SRR2183577 
sanchez_whole_chd4_216h_SRR2183578 
sanchez_whole_chd4_216h_SRR2183579 
sanchez_whole_chd4_288h_SRR2183580 
sanchez_whole_chd4_288h_SRR2183581 
sanchez_whole_chd4_288h_SRR2183582 
sanchez_whole_chd4_360h_SRR2183583 
sanchez_whole_chd4_360h_SRR2183584 
sanchez_whole_chd4_360h_SRR2183585 
sanchez_whole_mll_216h_SRR2658130 
sanchez_whole_mll_216h_SRR2658131 
sanchez_whole_mll_216h_SRR2658132
sanchez_whole_mll_216h_SRR2658133 
sanchez_whole_mll_288h_SRR2658126 
sanchez_whole_mll_288h_SRR2658127 
sanchez_whole_mll_288h_SRR2658128 			
sanchez_whole_mll_288h_SRR2658129 
sanchez_whole_p53_072h_SRR2183586 
sanchez_whole_p53_072h_SRR2183587 			
sanchez_whole_p53_072h_SRR2183588 			
sanchez_whole_p53_144h_SRR2183589 
sanchez_whole_p53_144h_SRR2183590 
sanchez_whole_p53_144h_SRR2183591 				
sanchez_whole_p53_216h_SRR2183592 
sanchez_whole_p53_216h_SRR2183593 	
sanchez_whole_p53_216h_SRR2183594 
sanchez_whole_p53_288h_SRR2183595 			
sanchez_whole_p53_288h_SRR2183596 
sanchez_whole_p53_288h_SRR2183597 	
sanchez_whole_p53_360h_SRR2183598	
sanchez_whole_p53_360h_SRR2183599 	
sanchez_whole_p53_360h_SRR2183600 
sanchez_whole_p53_432h_SRR2183601 				
sanchez_whole_p53_432h_SRR2183602 				
sanchez_whole_set_144h_SRR2658086 
sanchez_whole_set_144h_SRR2658087 	
sanchez_whole_set_144h_SRR2658088 
sanchez_whole_set_144h_SRR2658089 
sanchez_whole_set_216h_SRR2658094	
sanchez_whole_set_216h_SRR2658095 			
sanchez_whole_set_216h_SRR2658096 				
sanchez_whole_set_216h_SRR2658097		 
sanchez_whole_unc22_072h_SRR2183603 
sanchez_whole_unc22_072h_SRR2183604 				sanchez_whole_unc22_072h_SRR2183605 
sanchez_whole_unc22_144h_SRR2183606 
sanchez_whole_unc22_144h_SRR2183607 				
sanchez_whole_unc22_144h_SRR2183608 				
sanchez_whole_unc22_144h_SRR2658102 
sanchez_whole_unc22_144h_SRR2658103 
sanchez_whole_unc22_144h_SRR2658104 					
sanchez_whole_unc22_144h_SRR2658105 
sanchez_whole_unc22_216h_SRR2183609 
sanchez_whole_unc22_216h_SRR2183610 				
sanchez_whole_unc22_216h_SRR2183611 				
sanchez_whole_unc22_216h_SRR2658110 
sanchez_whole_unc22_216h_SRR2658111 
sanchez_whole_unc22_216h_SRR2658112 
sanchez_whole_unc22_216h_SRR2658113 
sanchez_whole_unc22_216h_SRR2658138 
sanchez_whole_unc22_216h_SRR2658139 
sanchez_whole_unc22_216h_SRR2658140 
sanchez_whole_unc22_216h_SRR2658141 
sanchez_whole_unc22_288h_SRR2183612 
sanchez_whole_unc22_288h_SRR2183613 
sanchez_whole_unc22_288h_SRR2183614 
sanchez_whole_unc22_288h_SRR2658134 
sanchez_whole_unc22_288h_SRR2658135 
sanchez_whole_unc22_288h_SRR2658136 
sanchez_whole_unc22_288h_SRR2658137 
sanchez_whole_unc22_360h_SRR2183615 
sanchez_whole_unc22_360h_SRR2183616 
sanchez_whole_unc22_360h_SRR2183617 
sanchez_whole_unc22_432h_SRR2183618 
sanchez_whole_unc22_432h_SRR2183619 
sanchez_whole_unc22_432h_SRR2183620 			
sanchez_x1_mll_216h_SRR2658082 			
sanchez_x1_mll_216h_SRR2658083 			
sanchez_x1_mll_216h_SRR2658084 		
sanchez_x1_mll_216h_SRR2658085 		
sanchez_x1_mll_288h_SRR2658078 		
sanchez_x1_mll_288h_SRR2658079 		
sanchez_x1_mll_288h_SRR2658080 		
sanchez_x1_mll_288h_SRR2658081 			
sanchez_x1_na_na_SRR2407874 		
sanchez_x1_na_na_SRR2407875 
sanchez_x1_na_na_SRR2407876 			
sanchez_x1_na_na_SRR2407877 			
sanchez_x1_set_144h_SRR2658090 			
sanchez_x1_set_144h_SRR2658091 			
sanchez_x1_set_144h_SRR2658092 		
sanchez_x1_set_144h_SRR2658093 		
sanchez_x1_set_216h_SRR2658098 			
sanchez_x1_set_216h_SRR2658099
sanchez_x1_set_216h_SRR2658100 
sanchez_x1_set_216h_SRR2658101 
sanchez_x1_unc22_144h_SRR2658106 
sanchez_x1_unc22_144h_SRR2658107 
sanchez_x1_unc22_144h_SRR2658108 
sanchez_x1_unc22_144h_SRR2658109 
sanchez_x1_unc22_216h_SRR2658114 
sanchez_x1_unc22_216h_SRR2658115 
sanchez_x1_unc22_216h_SRR2658116 
sanchez_x1_unc22_216h_SRR2658117 
sanchez_x1_unc22_216h_SRR2658122 
sanchez_x1_unc22_216h_SRR2658123 
sanchez_x1_unc22_216h_SRR2658124 
sanchez_x1_unc22_216h_SRR2658125 
sanchez_x1_unc22_288h_SRR2658118 
sanchez_x1_unc22_288h_SRR2658119 
sanchez_x1_unc22_288h_SRR2658120 
sanchez_x1_unc22_288h_SRR2658121 
sanchez_xins_na_na_SRR2407878 
sanchez_xins_na_na_SRR2407879
sanchez_xins_na_na_SRR240788
sanchez_xins_na_na_SRR2407881