SRX23948494 Ath_cDNA_ONT_rep1 SRP495197 PRJNA1087576 For ONT libraries RNA was converted to cDNA using Mint cDNA synthesis kit (Evrogen, Moscow, Russia) with 18 cycles of amplification with the following modification: 1) cDNA synthesis is primed with oligonucleotides that contain not only dT part and adapter part but also custom barcode, specific for each sample; 2) optimal number of cycles for amplification was selected based on the results of qPCR with primers annealing at 3 and 5 ends. The number of cycles falling to the upper part of linear phase was considered to be optimal. Amplified cDNA was used as input for library preparation using standard protocol for genomic DNA with LSK-109 kit. Libraries were sequenced on PromethION instrument using R9.4.1 flowcell. SRS20750210 SAMN40449987 Ath_cDNA_ONT_rep1 RNA-Seq TRANSCRIPTOMIC PolyA PromethION SRX23948495 Ath_cDNA_ONT_rep2 SRP495197 PRJNA1087576 For ONT libraries RNA was converted to cDNA using Mint cDNA synthesis kit (Evrogen, Moscow, Russia) with 18 cycles of amplification with the following modification: 1) cDNA synthesis is primed with oligonucleotides that contain not only dT part and adapter part but also custom barcode, specific for each sample; 2) optimal number of cycles for amplification was selected based on the results of qPCR with primers annealing at 3 and 5 ends. The number of cycles falling to the upper part of linear phase was considered to be optimal. Amplified cDNA was used as input for library preparation using standard protocol for genomic DNA with LSK-109 kit. Libraries were sequenced on PromethION instrument using R9.4.1 flowcell. SRS20750211 SAMN40449988 Ath_cDNA_ONT_rep2 RNA-Seq TRANSCRIPTOMIC PolyA PromethION SRX23948496 Ath_cDNA_ONT_rep3 SRP495197 PRJNA1087576 For ONT libraries RNA was converted to cDNA using Mint cDNA synthesis kit (Evrogen, Moscow, Russia) with 18 cycles of amplification with the following modification: 1) cDNA synthesis is primed with oligonucleotides that contain not only dT part and adapter part but also custom barcode, specific for each sample; 2) optimal number of cycles for amplification was selected based on the results of qPCR with primers annealing at 3 and 5 ends. The number of cycles falling to the upper part of linear phase was considered to be optimal. Amplified cDNA was used as input for library preparation using standard protocol for genomic DNA with LSK-109 kit. Libraries were sequenced on PromethION instrument using R9.4.1 flowcell. SRS20750212 SAMN40449989 Ath_cDNA_ONT_rep3 RNA-Seq TRANSCRIPTOMIC PolyA PromethION SRX23948497 Ath_CAGE_rep1 SRP495197 PRJNA1087576 RNA is processed as described in Murata et al. 2014. SRS20750210 SAMN40449987 Ath_CAGE_rep1 RNA-Seq TRANSCRIPTOMIC CAGE NextSeq 500 SRX23948498 Ath_CAGE_rep2 SRP495197 PRJNA1087576 RNA is processed as described in Murata et al. 2014. SRS20750211 SAMN40449988 Ath_CAGE_rep2 RNA-Seq TRANSCRIPTOMIC CAGE NextSeq 500 SRX23948499 Ath_CAGE_rep3 SRP495197 PRJNA1087576 RNA is processed as described in Murata et al. 2014. SRS20750212 SAMN40449989 Ath_CAGE_rep3 RNA-Seq TRANSCRIPTOMIC CAGE NextSeq 500