SRX2511763 GSM2465795 SRP097638 SRS1935456 GSM2465795 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index ATCACG sequenced on 03/11/16 (40x40), 03/31/16 (100x100) and 04/13/16 (50x50). Illumina HiSeq 2000 gds 302465795 GEO Accession GSM2465795 SRX2511764 GSM2465796 SRP097638 SRS1935457 GSM2465796 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index TTAGGC sequenced on 03/11/16 (40x40), 03/31/16 (100x100) and 04/13/16 (50x50). Illumina HiSeq 2000 gds 302465796 GEO Accession GSM2465796 SRX2511765 GSM2465797 SRP097638 SRS1935458 GSM2465797 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index CGATGT sequenced on 03/11/16 (40x40), 03/31/16 (100x100) and 04/13/16 (50x50). Illumina HiSeq 2000 gds 302465797 GEO Accession GSM2465797 SRX2511766 GSM2465798 SRP097638 SRS1935459 GSM2465798 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index GATCAG sequenced on 03/11/16 (40x40), 03/31/16 (100x100) and 04/13/16 (50x50). Illumina HiSeq 2000 gds 302465798 GEO Accession GSM2465798 SRX2511767 GSM2465799 SRP097638 SRS1935460 GSM2465799 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index TGACCA sequenced on 03/11/16 (40x40), 03/31/16 (100x100) and 04/13/16 (50x50). Illumina HiSeq 2000 gds 302465799 GEO Accession GSM2465799 SRX2511768 GSM2465800 SRP097638 SRS1935461 GSM2465800 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index TAGCTT sequenced on 03/11/16 (40x40), 03/31/16 (100x100), and 04/13/16 (50x50). Illumina HiSeq 2000 gds 302465800 GEO Accession GSM2465800 SRX2511769 GSM2465801 SRP097638 SRS1935462 GSM2465801 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index ATCACG sequenced on 12/09/16. Illumina HiSeq 2000 gds 302465801 GEO Accession GSM2465801 SRX2511770 GSM2465802 SRP097638 SRS1935463 GSM2465802 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index ACAGTG sequenced on 12/09/16. Illumina HiSeq 2000 gds 302465802 GEO Accession GSM2465802 SRX2511771 GSM2465803 SRP097638 SRS1935464 GSM2465803 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index CGATGT sequenced on 12/09/16. Illumina HiSeq 2000 gds 302465803 GEO Accession GSM2465803 SRX2511772 GSM2465804 SRP097638 SRS1935465 GSM2465804 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index GCCAAT sequenced on 12/09/16 . Illumina HiSeq 2000 gds 302465804 GEO Accession GSM2465804 SRX2511773 GSM2465805 SRP097638 SRS1935466 GSM2465805 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol sequenced on 10/03/14 with index GCCAAT. Illumina HiSeq 2000 gds 302465805 GEO Accession GSM2465805 SRX2511774 GSM2465806 SRP097638 SRS1935467 GSM2465806 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol sequenced on 10/03/14 with index CTTGTA. Illumina HiSeq 2000 gds 302465806 GEO Accession GSM2465806 SRX2511775 GSM2465807 SRP097638 SRS1935468 GSM2465807 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol sequenced on 10/03/14 with index TAGCTT. Illumina HiSeq 2000 gds 302465807 GEO Accession GSM2465807 SRX2511776 GSM2465808 SRP097638 SRS1935469 GSM2465808 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol sequenced on 10/03/14 with index GGCTAC. Illumina HiSeq 2000 gds 302465808 GEO Accession GSM2465808 SRX2511777 GSM2465809 SRP097638 SRS1935470 GSM2465809 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index TTAGGC sequenced on 12/09/16. Illumina HiSeq 2000 gds 302465809 GEO Accession GSM2465809 SRX2511778 GSM2465810 SRP097638 SRS1935471 GSM2465810 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index CAGATC sequenced on 12/09/16. Illumina HiSeq 2000 gds 302465810 GEO Accession GSM2465810 SRX2511779 GSM2465811 SRP097638 SRS1935472 GSM2465811 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index CAGATC sequenced on 03/11/16 (40x 40), 03/31/16 (100x100) and 04/13/16 (50x50). Illumina HiSeq 2000 gds 302465811 GEO Accession GSM2465811 SRX2511780 GSM2465812 SRP097638 SRS1935473 GSM2465812 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index GGCTAC sequenced on 03/11/16 (40x40) , 03/31/16 (100x100) and 04/13/16 (50x50). Illumina HiSeq 2000 gds 302465812 GEO Accession GSM2465812 SRX2511781 GSM2465813 SRP097638 SRS1935474 GSM2465813 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index ACAGTG sequenced on 03/11/16 (40x40), 03/31/16 (100x100),and 04/13/16 (50x50). Illumina HiSeq 2000 gds 302465813 GEO Accession GSM2465813 SRX2511782 GSM2465814 SRP097638 SRS1935475 GSM2465814 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index GCCAAT sequenced on 03/11/16 (40x40), 03/31/16 (100x100) and 04/13/16 (50x50). Illumina HiSeq 2000 gds 302465814 GEO Accession GSM2465814 SRX2511783 GSM2465815 SRP097638 SRS1935476 GSM2465815 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index TGACCA sequenced on 12/09/16. Illumina HiSeq 2000 gds 302465815 GEO Accession GSM2465815 SRX2511784 GSM2465816 SRP097638 SRS1935477 GSM2465816 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index ACTTGA sequenced on 12/09/16. Illumina HiSeq 2000 gds 302465816 GEO Accession GSM2465816 SRX2511785 GSM2465817 SRP097638 SRS1935478 GSM2465817 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index ACTTGA sequenced on 03/11/16 (40x40) and 03/31/16 (100x100). Illumina HiSeq 2000 gds 302465817 GEO Accession GSM2465817 SRX2511786 GSM2465818 SRP097638 SRS1935479 GSM2465818 Bisulfite-Seq GENOMIC RANDOM Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads. Illumina TruSeq DNA methylation protocol with index CTTGTA sequenced on 03/11/16 (40x40) and 03/31/16 (100x100). Illumina HiSeq 2000 gds 302465818 GEO Accession GSM2465818 SRX2511787 GSM2465819 SRP097638 SRS1935480 GSM2465819 RNA-Seq TRANSCRIPTOMIC cDNA Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol. Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode TGACCA. Illumina HiSeq 2000 gds 302465819 GEO Accession GSM2465819 SRX2511788 GSM2465820 SRP097638 SRS1935481 GSM2465820 RNA-Seq TRANSCRIPTOMIC cDNA Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol. Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode CGATGT. Illumina HiSeq 2000 gds 302465820 GEO Accession GSM2465820 SRX2511789 GSM2465821 SRP097638 SRS1935482 GSM2465821 RNA-Seq TRANSCRIPTOMIC cDNA Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol. Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode CTTGTA. Illumina HiSeq 2000 gds 302465821 GEO Accession GSM2465821 SRX2511790 GSM2465822 SRP097638 SRS1935483 GSM2465822 RNA-Seq TRANSCRIPTOMIC cDNA Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol. Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode ACAGTG. Illumina HiSeq 2000 gds 302465822 GEO Accession GSM2465822 SRX2511791 GSM2465823 SRP097638 SRS1935484 GSM2465823 RNA-Seq TRANSCRIPTOMIC cDNA Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol. Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode AGTCAA. Illumina HiSeq 2000 gds 302465823 GEO Accession GSM2465823 SRX2511792 GSM2465824 SRP097638 SRS1935485 GSM2465824 RNA-Seq TRANSCRIPTOMIC cDNA Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol. Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode AGTTCC. Illumina HiSeq 2000 gds 302465824 GEO Accession GSM2465824 SRX2511793 GSM2465825 SRP097638 SRS1935486 GSM2465825 RNA-Seq TRANSCRIPTOMIC cDNA Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol. Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode GCCAAT. Illumina HiSeq 2000 gds 302465825 GEO Accession GSM2465825 SRX2511794 GSM2465826 SRP097638 SRS1935487 GSM2465826 RNA-Seq TRANSCRIPTOMIC cDNA Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol. Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode ATGTCA. Illumina HiSeq 2000 gds 302465826 GEO Accession GSM2465826 SRX2511795 GSM2465827 SRP097638 SRS1935488 GSM2465827 RNA-Seq TRANSCRIPTOMIC cDNA Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol. Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode CCGTCC. Illumina HiSeq 2000 gds 302465827 GEO Accession GSM2465827 SRX2511796 GSM2465828 SRP097638 SRS1935489 GSM2465828 RNA-Seq TRANSCRIPTOMIC cDNA Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol. Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode CAGATC. Illumina HiSeq 2000 gds 302465828 GEO Accession GSM2465828 SRX2511797 GSM2465829 SRP097638 SRS1935490 GSM2465829 RNA-Seq TRANSCRIPTOMIC cDNA Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol. Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode GTCCGC. Illumina HiSeq 2000 gds 302465829 GEO Accession GSM2465829 SRX2511798 GSM2465830 SRP097638 SRS1935491 GSM2465830 RNA-Seq TRANSCRIPTOMIC cDNA Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903). For RNA-seq, libraries were constructed from 1ug RNA using the RNA TruSeq stranded library kit (Illumina, uses polyA selection) using 15 cycles of amplification. Reads were sequenced on an Illumina HiSeq2000 using a 40bp single-end protocol. Illumina TruSeq RNA stranded protocol sequenced on 07/24/2015 with barcode GTGAAA. Illumina HiSeq 2000 gds 302465830 GEO Accession GSM2465830