ERX3358103 E-MTAB-7978:Sample 1_p E-MTAB-7978:Sample 1_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422977 SAMEA5618890 Sample 1_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage flower stage 15 Experimental Factor: organism part sepal Experimental Factor: sampling site not applicable ERX3358104 E-MTAB-7978:Sample 10_p E-MTAB-7978:Sample 10_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422978 SAMEA5618891 Sample 10_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part stem node Experimental Factor: sampling site first node ERX3358105 E-MTAB-7978:Sample 11_p E-MTAB-7978:Sample 11_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422979 SAMEA5618892 Sample 11_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part stem internode Experimental Factor: sampling site second internode ERX3358106 E-MTAB-7978:Sample 12_p E-MTAB-7978:Sample 12_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422980 SAMEA5618893 Sample 12_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part cauline leaf Experimental Factor: sampling site not applicable ERX3358107 E-MTAB-7978:Sample 13_p E-MTAB-7978:Sample 13_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422981 SAMEA5618894 Sample 13_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part rosette leaf Experimental Factor: sampling site rosette leaf 7 distal part ERX3358108 E-MTAB-7978:Sample 14_p E-MTAB-7978:Sample 14_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422982 SAMEA5618895 Sample 14_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part rosette leaf Experimental Factor: sampling site rosette leaf 7 proximal part ERX3358109 E-MTAB-7978:Sample 15_p E-MTAB-7978:Sample 15_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422983 SAMEA5618896 Sample 15_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part petiole Experimental Factor: sampling site rosette leaf 7 petiole ERX3358110 E-MTAB-7978:Sample 16_p E-MTAB-7978:Sample 16_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422984 SAMEA5618897 Sample 16_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part adult vascular leaf Experimental Factor: sampling site not applicable ERX3358111 E-MTAB-7978:Sample 17_p E-MTAB-7978:Sample 17_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422985 SAMEA5618898 Sample 17_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part root Experimental Factor: sampling site not applicable ERX3358112 E-MTAB-7978:Sample 18_p E-MTAB-7978:Sample 18_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422986 SAMEA5618899 Sample 18_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage flower stage 15 Experimental Factor: organism part flower pedicel Experimental Factor: sampling site not applicable ERX3358113 E-MTAB-7978:Sample 19_p E-MTAB-7978:Sample 19_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422987 SAMEA5618900 Sample 19_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage flower stage 15 Experimental Factor: organism part flower Experimental Factor: sampling site not applicable ERX3358114 E-MTAB-7978:Sample 2_p E-MTAB-7978:Sample 2_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422988 SAMEA5618901 Sample 2_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage flower stage 15 Experimental Factor: organism part petal Experimental Factor: sampling site not applicable ERX3358115 E-MTAB-7978:Sample 20_p E-MTAB-7978:Sample 20_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422989 SAMEA5618902 Sample 20_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part fruit septum Experimental Factor: sampling site not applicable ERX3358116 E-MTAB-7978:Sample 21_p E-MTAB-7978:Sample 21_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422990 SAMEA5618903 Sample 21_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part fruit valve Experimental Factor: sampling site not applicable ERX3358117 E-MTAB-7978:Sample 22_p E-MTAB-7978:Sample 22_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422991 SAMEA5618904 Sample 22_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage callus Experimental Factor: organism part plant callus Experimental Factor: sampling site not applicable ERX3358118 E-MTAB-7978:Sample 23_p E-MTAB-7978:Sample 23_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422992 SAMEA5618905 Sample 23_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage callus Experimental Factor: organism part plant callus Experimental Factor: sampling site not applicable ERX3358119 E-MTAB-7978:Sample 24_p E-MTAB-7978:Sample 24_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422993 SAMEA5618906 Sample 24_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage cell culture Experimental Factor: organism part root Experimental Factor: sampling site not applicable ERX3358120 E-MTAB-7978:Sample 25_p E-MTAB-7978:Sample 25_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422994 SAMEA5618907 Sample 25_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage cell culture Experimental Factor: organism part root Experimental Factor: sampling site not applicable ERX3358121 E-MTAB-7978:Sample 26_p E-MTAB-7978:Sample 26_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422995 SAMEA5618908 Sample 26_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage seedling Experimental Factor: organism part cotyledon Experimental Factor: sampling site not applicable ERX3358122 E-MTAB-7978:Sample 27_p E-MTAB-7978:Sample 27_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422996 SAMEA5618909 Sample 27_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage seedling Experimental Factor: organism part hypocotyl Experimental Factor: sampling site not applicable ERX3358123 E-MTAB-7978:Sample 28_p E-MTAB-7978:Sample 28_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422997 SAMEA5618910 Sample 28_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage seedling Experimental Factor: organism part root tip Experimental Factor: sampling site not applicable ERX3358124 E-MTAB-7978:Sample 29_p E-MTAB-7978:Sample 29_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422998 SAMEA5618911 Sample 29_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage seedling Experimental Factor: organism part root tip Experimental Factor: sampling site upper zone ERX3358125 E-MTAB-7978:Sample 3_p E-MTAB-7978:Sample 3_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3422999 SAMEA5618912 Sample 3_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage flower stage 15 Experimental Factor: organism part stamen Experimental Factor: sampling site not applicable ERX3358126 E-MTAB-7978:Sample 30_p E-MTAB-7978:Sample 30_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423000 SAMEA5618913 Sample 30_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage seedling Experimental Factor: organism part mixed shoot apical meristem, cotyledon and first leaves Experimental Factor: sampling site not applicable ERX3358127 E-MTAB-7978:Sample 31_p E-MTAB-7978:Sample 31_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423001 SAMEA5618914 Sample 31_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part cotyledon Experimental Factor: sampling site not applicable ERX3358128 E-MTAB-7978:Sample 32_p E-MTAB-7978:Sample 32_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423002 SAMEA5618915 Sample 32_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part rosette leaf Experimental Factor: sampling site rosette leaf 1 ERX3358129 E-MTAB-7978:Sample 33_p E-MTAB-7978:Sample 33_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423003 SAMEA5618916 Sample 33_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part rosette leaf Experimental Factor: sampling site rosette leaf 2 ERX3358130 E-MTAB-7978:Sample 34_p E-MTAB-7978:Sample 34_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423004 SAMEA5618917 Sample 34_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part rosette leaf Experimental Factor: sampling site rosette leaf 3 ERX3358131 E-MTAB-7978:Sample 35_p E-MTAB-7978:Sample 35_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423005 SAMEA5618918 Sample 35_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part rosette leaf Experimental Factor: sampling site rosette leaf 4 ERX3358132 E-MTAB-7978:Sample 36_p E-MTAB-7978:Sample 36_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423006 SAMEA5618919 Sample 36_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part rosette leaf Experimental Factor: sampling site rosette leaf 5 ERX3358133 E-MTAB-7978:Sample 37_p E-MTAB-7978:Sample 37_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423007 SAMEA5618920 Sample 37_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part rosette leaf Experimental Factor: sampling site rosette leaf 6 ERX3358134 E-MTAB-7978:Sample 38_p E-MTAB-7978:Sample 38_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423008 SAMEA5618921 Sample 38_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part rosette leaf Experimental Factor: sampling site rosette leaf 7 ERX3358135 E-MTAB-7978:Sample 39_p E-MTAB-7978:Sample 39_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423009 SAMEA5618922 Sample 39_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part rosette leaf Experimental Factor: sampling site rosette leaf 8 ERX3358136 E-MTAB-7978:Sample 4_p E-MTAB-7978:Sample 4_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423010 SAMEA5618923 Sample 4_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage flower stage 15 Experimental Factor: organism part carpel Experimental Factor: sampling site not applicable ERX3358137 E-MTAB-7978:Sample 40_p E-MTAB-7978:Sample 40_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423011 SAMEA5618924 Sample 40_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part rosette leaf Experimental Factor: sampling site rosette leaf 9 ERX3358138 E-MTAB-7978:Sample 41_p E-MTAB-7978:Sample 41_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423012 SAMEA5618925 Sample 41_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part rosette leaf Experimental Factor: sampling site rosette leaf 10 ERX3358139 E-MTAB-7978:Sample 42_p E-MTAB-7978:Sample 42_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423013 SAMEA5618926 Sample 42_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part rosette leaf Experimental Factor: sampling site rosette leaf 11 ERX3358140 E-MTAB-7978:Sample 43_p E-MTAB-7978:Sample 43_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423014 SAMEA5618927 Sample 43_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage adult Experimental Factor: organism part rosette leaf Experimental Factor: sampling site rosette leaf 12 ERX3358141 E-MTAB-7978:Sample 44_p E-MTAB-7978:Sample 44_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423015 SAMEA5618928 Sample 44_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage flower stage 9 Experimental Factor: organism part flower Experimental Factor: sampling site not applicable ERX3358142 E-MTAB-7978:Sample 45_p E-MTAB-7978:Sample 45_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423016 SAMEA5618929 Sample 45_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage flower stage 10 Experimental Factor: organism part flower Experimental Factor: sampling site not applicable ERX3358143 E-MTAB-7978:Sample 46_p E-MTAB-7978:Sample 46_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423017 SAMEA5618930 Sample 46_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage flower stage 11 Experimental Factor: organism part flower Experimental Factor: sampling site not applicable ERX3358144 E-MTAB-7978:Sample 47_p E-MTAB-7978:Sample 47_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423018 SAMEA5618931 Sample 47_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage flower stage 12 Experimental Factor: organism part flower Experimental Factor: sampling site not applicable ERX3358145 E-MTAB-7978:Sample 48_p E-MTAB-7978:Sample 48_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423019 SAMEA5618932 Sample 48_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage flower stage 13 Experimental Factor: organism part flower Experimental Factor: sampling site not applicable ERX3358146 E-MTAB-7978:Sample 49_p E-MTAB-7978:Sample 49_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423020 SAMEA5618933 Sample 49_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage silique stage 1 Experimental Factor: organism part silique Experimental Factor: sampling site not applicable ERX3358147 E-MTAB-7978:Sample 5_p E-MTAB-7978:Sample 5_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423021 SAMEA5618934 Sample 5_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage silique stage 3 Experimental Factor: organism part silique Experimental Factor: sampling site not applicable ERX3358148 E-MTAB-7978:Sample 50_p E-MTAB-7978:Sample 50_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423022 SAMEA5618935 Sample 50_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage silique stage 2 Experimental Factor: organism part silique Experimental Factor: sampling site not applicable ERX3358149 E-MTAB-7978:Sample 51_p E-MTAB-7978:Sample 51_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423023 SAMEA5618936 Sample 51_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage silique stage 4 Experimental Factor: organism part silique Experimental Factor: sampling site not applicable ERX3358150 E-MTAB-7978:Sample 52_p E-MTAB-7978:Sample 52_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423024 SAMEA5618937 Sample 52_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage silique stage 5 Experimental Factor: organism part silique Experimental Factor: sampling site not applicable ERX3358151 E-MTAB-7978:Sample 53_p E-MTAB-7978:Sample 53_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423025 SAMEA5618938 Sample 53_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage embryo stage 6 Experimental Factor: organism part seed Experimental Factor: sampling site not applicable ERX3358152 E-MTAB-7978:Sample 54_p E-MTAB-7978:Sample 54_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423026 SAMEA5618939 Sample 54_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage embryo stage 7 Experimental Factor: organism part seed Experimental Factor: sampling site not applicable ERX3358153 E-MTAB-7978:Sample 55_p E-MTAB-7978:Sample 55_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423027 SAMEA5618940 Sample 55_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage embryo stage 8 Experimental Factor: organism part seed Experimental Factor: sampling site not applicable ERX3358154 E-MTAB-7978:Sample 56_p E-MTAB-7978:Sample 56_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423028 SAMEA5618941 Sample 56_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage embryo stage 9 Experimental Factor: organism part seed Experimental Factor: sampling site not applicable ERX3358155 E-MTAB-7978:Sample 6_p E-MTAB-7978:Sample 6_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423029 SAMEA5618942 Sample 6_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage embryo stage 10 Experimental Factor: organism part seed Experimental Factor: sampling site not applicable ERX3358156 E-MTAB-7978:Sample 7_p E-MTAB-7978:Sample 7_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423030 SAMEA5618943 Sample 7_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage dry seed stage Experimental Factor: organism part seed Experimental Factor: sampling site not applicable ERX3358157 E-MTAB-7978:Sample 8_p E-MTAB-7978:Sample 8_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423031 SAMEA5618944 Sample 8_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage seed imbibition stage Experimental Factor: organism part seed Experimental Factor: sampling site not applicable ERX3358158 E-MTAB-7978:Sample 9_p E-MTAB-7978:Sample 9_p ERP115370 PRJEB32665 Arabidopsis tissue atlas ERS3423032 SAMEA5618945 Sample 9_p RNA-Seq TRANSCRIPTOMIC PolyA Tissues were collected at the desired growth stage, pooled, snap-frozen in liquid nitrogen and homogenized to a fine powder. Arabidopsis thaliana wild type (Columbia-0) plants were grown on soil or MS media respectively. Total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany). DNA was remove by on-column treatment with rDNAse (Macherey-Nagel, Düren, Germany). For recalcitrant samples (seed, silique, pollen), we adopted a LiCl-based protocol with minor modifications (Onate-Sanchez and Vicente-Carbajosa, 2008). After LiCl precipitation the RNA pellet was dissolved in rDNAse buffer (Macherey-Nagel, Düren, Germany) and treated with rDNAse (Macherey-Nagel, Düren, Germany). The final pellet was re-suspended in DEPC-treated water. cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Ilumina, San Diego, CA, USA) according to the manufacturer's instructions. Illumina HiSeq 2500 Experimental Factor: developmental stage flower stage 15 Experimental Factor: organism part pollen Experimental Factor: sampling site not applicable