Supplemental Table 1. RNA-Seq Data Sources Used for Transcript Assemblies. Ninety-five RNA-Seq data were downloaded from the NCBI's sequence read archive (http://www.ncbi.nlm.nih.gov/sra). One data set was described by Takacs et al (2012), and may be obtained from the authors. All RNA-seq data were used to generate individual transcript assemblies. SRA Study ID SRA Run IDs/Other ID Description PubMed ID SRP011991 SRA Experiment ID SRX114632 SRR397772 SRR397771 NA SRP011991 SRX114630 SRR396679 SRR396678 SRP011929 SRX131448 SRR448121 SRP011929 SRX131447 SRR448119 SRP011566 SRX130104 SRR445935 SRP011480 SRX129815 SRR445657 SRP011480 SRX129814 SRR445656 SRP011480 SRX129813 SRR445655 SRP011480 SRX129799 SRR445641 SRP011480 SRX129798 SRR445640 SRP011480 SRX129797 SRR445639 SRP011480 SRX129796 SRR445638 Seedling shoots, 14 days old, Mo17 x B73 and B73 x Mo17 hybrids Mo17 x B73 endosperm tissue, 10 days postpollination W22 immature tassel W22 immature ear Miami White 14-day old leaf tissue Tzi8 immature tassel Tzi8 seedling shoot tissue Tzi8 seedling root tissue Oh43 immature tassel Oh43 seedling shoot tissue Oh43 seedling root tissue Oh43 immature, NA NA NA NA NA NA NA NA NA NA NA SRP011480 SRX129693 SRR445385 SRP011480 SRX129692 SRR445384 SRP011480 SRX129690 SRR445383 SRP011480 SRX129689 SRR445382 SRP010139 SRX114583 SRR396617 SRR396616 SRP010124 SRX114231 SRR395266 SRR395267 SRP010124 SRX114230 SRP010124 SRX114228 SRP009313 SRX105679 SRR395193 SRR395209 SRR395210 SRR395211 SRR395191 SRR395192 SRR395194 SRR395208 SRR364454 SRP009313 SRX105666 SRP009313 SRX105662 SRP009313 SRX105657 SRP009313 SRX105655 SRP006965 SRX072646 SRP006965 SRX072636 SRR364439 SRR364437 SRR364436 SRR364435 SRR364433 SRR364432 SRR364428 SRR364427 SRR364426 SRR364429 SRR364430 SRR364431 SRR254176 SRR254169 SRR255405 unpollinated ear tip B97 seedling root tissue B97 immature, unpollinated ear tip B73 immature tassel B73 seedling shoot tissue Lower leaves of glossy3 wildtype and mutant at 2leaf stage Mo17 x B73 primary root tissue B73 x Mo17 primary root tissue NA NA NA NA 22731681 NA NA B73 primary root tissue NA Mo73 x B73 endosperm tissue Mo17 embryo tissue 22198147 B73 embryo tissue 22198147 B73 endosperm tissue Mo17 endosperm tissue B73 embryo sac tissue B73 mature 22198147 22198147 22198147 NA NA SRP006965 SRX072635 SRP006703 SRX061107 SRR250416 SRR250415 SRR248565 SRR242505 SRR197051 SRP006703 SRX061007 SRR197049 SRP006703 SRX061006 SRR197048 SRP006703 SRX061005 SRR197047 SRP006703 SRX061004 SRR197046 SRP006703 SRX061003 SRR197045 SRP006703 SRX061002 SRR197044 SRP006703 SRX061001 SRR197043 SRP006703 SRX061000 SRR197042 SRP006703 SRX060999 SRR197041 SRP006703 SRX060998 SRR197037 SRP006703 SRX060997 SRR197034 SRP006703 SRX060996 SRR197033 SRP006703 SRX060995 SRR197032 SRP006703 SRX060994 SRR197031 pollen B73 seedling tissue NC358 seedling tissues B14A seedling tissues PHG47 seedling tissues W605S seedling tissues MS71 seedling tissues CML333 seedling tissues Mo17 seedling tissues B37 seedling tissues PHW65 seedling tissues B73 seedling tissues B97 seedling tissues M37W seedling tissues Oh43 seedling tissues PHN11 seedling tissues CML103 seedling tissues NA 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 SRP006703 SRX060993 SRR197030 SRP006703 SRX060992 SRR197029 SRP006703 SRX060991 SRR197028 SRP006703 SRX060990 SRR197027 SRP006703 SRX060989 SRR197026 SRP006703 SRX060988 SRR197025 SRP006703 SRX060987 SRR197024 SRP006703 SRX060986 SRR197023 SRP006703 SRX060985 SRR197022 SRP006703 SRX060984 SRR197021 SRP006703 SRX060983 SRR197020 SRP006703 SRX060982 SRR197019 SRP006703 SRX060981 SRR197018 SRP006703 SRX060980 SRR197017 SRP006703 SRX060979 SRR197016 SRP006703 SRX060978 SRR197015 SRP006703 SRX060977 SRR197013 CML322 seedling tissues W64A seedling tissues NC350 seedling tissues Oh7B seedling tissues H99 seedling tissues NC358 seedling tissues MoG seedling tissues B14A seedling tissues PHG47 seedling tissues W605S seedling tissues MS71 seedling tissues CML333 seedling tissues Mo17 seedling tissues B37 seedling tissues PHW65 seedling tissues B73 seedling tissues RSG_11_1 seedling 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 SRP006703 SRX060976 SRR197012 SRP006703 SRX060975 SRR197011 SRP006703 SRX060974 SRR197010 SRP006703 SRX060973 SRR197009 SRP006703 SRX060972 SRR197008 SRP006703 SRX060971 SRR197007 SRP006703 SRX060969 SRR197006 SRP006703 SRX060968 SRR197005 SRP006703 SRX060965 SRR197004 SRP006463 SRX058608 SRR189773 SRP006463 SRX058607 SRR189772 SRP006463 SRP006463 SRX058606 SRX058605 SRR189771 SRR189770 SRP006463 SRX058604 SRR189769 SRP006463 SRX058603 SRR189768 SRP006463 SRX058602 SRR393018 SRP006463 SRX058601 SRR393017 tissues M37W seedling tissues Oh43 seedling tissues PHN11 seedling tissues CML103 seedling tissues CML322 seedling tissues W64A seedling tissues NC350 seedling tissues Oh7B seedling tissues H99 seedling tissues B73 seed, 10 days postpollination B73 mature silk tissue B73 pollen B73 ovule tissue B73 whole anthers B73 endosperm, 25 days postpollination B73 endosperm, 25 days postpollination B73 seed, 5 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 22438891 NA NA NA NA NA NA NA NA SRP006463 SRX058600 SRR393016 SRP006463 SRX058599 SRR189763 SRP006463 SRX058598 SRR189762 SRP006463 SRX058597 SRR189760 SRP006463 SRX058596 SRR189761 SRP005995 SRX047544 SRR124825 SRP002265 SRX018907 SRR039512 SRR039514 SRP002265 SRX018905 SRR039509 SRR039510 SRP002265 SRX018904 SRP002265 SRX018903 SRP002265 SRX018902 SRP002265 SRX018901 SRP001550 SRX014791 SRX014790 SRR039507 SRR039508 SRR039505 SRR039506 SRR039503 SRR039504 SRR039501 SRR039502 SRR032085 SRR032086 SRR032083 SRR032084 SRP001477 SRX013981 SRX013982 SRR031087 SRR031088 SRP001359 SRX012381 SRP001359 SRX012380 SRR029381 SRR029382 SRR029373 days postpollination B73 postpollination tassel B73 postemergence cob tissue B73 preemergence tassel B73 preemergence cob tissue B73 20-day old seedling Mo17 x B73 endosperm, 10 days postpollination B73 leaf bundle sheath cells B73 leaf mesophyll cells B73 leaf tip B73 leaf 4 cm section B73 leaf 1 cm section B73 leaf basal section Mop1/mop1 and mop1/mop1 shoot apical meristems Mo17 x B73 and B73 x Mo17 14 day old seedlings B73 root tissue B73 shoot NA NA NA NA NA NA NA NA NA NA NA NA 19936292 19965432 19376930 19376930 SRP001315 SRX012274 SRP001315 SRX012273 SRR029374 SRR029158 SRR029185 SRR029186 SRR029188 SRR029189 SRR029190 SRR029191 SRR029177 SRR029178 SRR029179 SRR029180 SRR029181 SRR029182 SRR029183 SRR029184 10214045_6148NAAXX tissue Mo17 leaf tip NA Mo17 leaf base NA Shoot apical meristem tissue 22911570
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