SRX6102429 GSM3900879 SRP202206 SRS5002886 GSM3900879 RNA-Seq TRANSCRIPTOMIC cDNA PlaNET-Seq: Nuclei were isolated from 3 grams of seedlings. Chromatin was solubilized by DNase I treatment. Nascent RNA fraction was enriched by immunoprecipitation of FLAG-tagged RNAPII elongation complexes using anti-FLAG antibody (F3165, Sigma-Aldrich) coupled to Dynabeads Protein G. Finally, RNAPII complexes were eluted from Dynabeads by 3xFLAG peptide, and the nascent RNA was purified using miRNeasy kit (QIAgen). RNA-Seq: total RNA was isolated from seedlings using QIAgen Plant RNeasy kit. PlaNET-Seq: NGS libraries were constructed from nascent RNA using Small RNA-Seq Kit v3 (Bioo Scientific). The original protocol was modified to incorporate alkaline RNA fragmentation step after 3' adapter ligation. RNA-Seq: polyA-enriched libraries were constructed using Illumina TruSeq RNA Sample Prep Kit v2. Illumina HiSeq 4000 gds 303900879 GSM3900879 GEO Accession GSM3900879 SRX6102430 GSM3900880 SRP202206 SRS5002885 GSM3900880 RNA-Seq TRANSCRIPTOMIC cDNA PlaNET-Seq: Nuclei were isolated from 3 grams of seedlings. Chromatin was solubilized by DNase I treatment. Nascent RNA fraction was enriched by immunoprecipitation of FLAG-tagged RNAPII elongation complexes using anti-FLAG antibody (F3165, Sigma-Aldrich) coupled to Dynabeads Protein G. Finally, RNAPII complexes were eluted from Dynabeads by 3xFLAG peptide, and the nascent RNA was purified using miRNeasy kit (QIAgen). RNA-Seq: total RNA was isolated from seedlings using QIAgen Plant RNeasy kit. PlaNET-Seq: NGS libraries were constructed from nascent RNA using Small RNA-Seq Kit v3 (Bioo Scientific). The original protocol was modified to incorporate alkaline RNA fragmentation step after 3' adapter ligation. RNA-Seq: polyA-enriched libraries were constructed using Illumina TruSeq RNA Sample Prep Kit v2. Illumina HiSeq 4000 gds 303900880 GSM3900880 GEO Accession GSM3900880 SRX6102431 GSM3900881 SRP202206 SRS5002887 GSM3900881 RNA-Seq TRANSCRIPTOMIC cDNA PlaNET-Seq: Nuclei were isolated from 3 grams of seedlings. Chromatin was solubilized by DNase I treatment. Nascent RNA fraction was enriched by immunoprecipitation of FLAG-tagged RNAPII elongation complexes using anti-FLAG antibody (F3165, Sigma-Aldrich) coupled to Dynabeads Protein G. Finally, RNAPII complexes were eluted from Dynabeads by 3xFLAG peptide, and the nascent RNA was purified using miRNeasy kit (QIAgen). RNA-Seq: total RNA was isolated from seedlings using QIAgen Plant RNeasy kit. PlaNET-Seq: NGS libraries were constructed from nascent RNA using Small RNA-Seq Kit v3 (Bioo Scientific). The original protocol was modified to incorporate alkaline RNA fragmentation step after 3' adapter ligation. RNA-Seq: polyA-enriched libraries were constructed using Illumina TruSeq RNA Sample Prep Kit v2. Illumina HiSeq 4000 gds 303900881 GSM3900881 GEO Accession GSM3900881 SRX6102432 GSM3900882 SRP202206 SRS5002888 GSM3900882 RNA-Seq TRANSCRIPTOMIC cDNA PlaNET-Seq: Nuclei were isolated from 3 grams of seedlings. Chromatin was solubilized by DNase I treatment. Nascent RNA fraction was enriched by immunoprecipitation of FLAG-tagged RNAPII elongation complexes using anti-FLAG antibody (F3165, Sigma-Aldrich) coupled to Dynabeads Protein G. Finally, RNAPII complexes were eluted from Dynabeads by 3xFLAG peptide, and the nascent RNA was purified using miRNeasy kit (QIAgen). RNA-Seq: total RNA was isolated from seedlings using QIAgen Plant RNeasy kit. PlaNET-Seq: NGS libraries were constructed from nascent RNA using Small RNA-Seq Kit v3 (Bioo Scientific). The original protocol was modified to incorporate alkaline RNA fragmentation step after 3' adapter ligation. RNA-Seq: polyA-enriched libraries were constructed using Illumina TruSeq RNA Sample Prep Kit v2. Illumina HiSeq 4000 gds 303900882 GSM3900882 GEO Accession GSM3900882 SRX6102433 GSM3900883 SRP202206 SRS5002889 GSM3900883 RNA-Seq TRANSCRIPTOMIC cDNA PlaNET-Seq: Nuclei were isolated from 3 grams of seedlings. Chromatin was solubilized by DNase I treatment. Nascent RNA fraction was enriched by immunoprecipitation of FLAG-tagged RNAPII elongation complexes using anti-FLAG antibody (F3165, Sigma-Aldrich) coupled to Dynabeads Protein G. Finally, RNAPII complexes were eluted from Dynabeads by 3xFLAG peptide, and the nascent RNA was purified using miRNeasy kit (QIAgen). RNA-Seq: total RNA was isolated from seedlings using QIAgen Plant RNeasy kit. PlaNET-Seq: NGS libraries were constructed from nascent RNA using Small RNA-Seq Kit v3 (Bioo Scientific). The original protocol was modified to incorporate alkaline RNA fragmentation step after 3' adapter ligation. RNA-Seq: polyA-enriched libraries were constructed using Illumina TruSeq RNA Sample Prep Kit v2. Illumina HiSeq 4000 gds 303900883 GSM3900883 GEO Accession GSM3900883 SRX6102434 GSM3900884 SRP202206 SRS5002890 GSM3900884 RNA-Seq TRANSCRIPTOMIC cDNA PlaNET-Seq: Nuclei were isolated from 3 grams of seedlings. Chromatin was solubilized by DNase I treatment. Nascent RNA fraction was enriched by immunoprecipitation of FLAG-tagged RNAPII elongation complexes using anti-FLAG antibody (F3165, Sigma-Aldrich) coupled to Dynabeads Protein G. Finally, RNAPII complexes were eluted from Dynabeads by 3xFLAG peptide, and the nascent RNA was purified using miRNeasy kit (QIAgen). RNA-Seq: total RNA was isolated from seedlings using QIAgen Plant RNeasy kit. PlaNET-Seq: NGS libraries were constructed from nascent RNA using Small RNA-Seq Kit v3 (Bioo Scientific). The original protocol was modified to incorporate alkaline RNA fragmentation step after 3' adapter ligation. RNA-Seq: polyA-enriched libraries were constructed using Illumina TruSeq RNA Sample Prep Kit v2. Illumina HiSeq 4000 gds 303900884 GSM3900884 GEO Accession GSM3900884 SRX6102435 GSM3900885 SRP202206 SRS5002891 GSM3900885 RNA-Seq TRANSCRIPTOMIC cDNA PlaNET-Seq: Nuclei were isolated from 3 grams of seedlings. Chromatin was solubilized by DNase I treatment. Nascent RNA fraction was enriched by immunoprecipitation of FLAG-tagged RNAPII elongation complexes using anti-FLAG antibody (F3165, Sigma-Aldrich) coupled to Dynabeads Protein G. Finally, RNAPII complexes were eluted from Dynabeads by 3xFLAG peptide, and the nascent RNA was purified using miRNeasy kit (QIAgen). RNA-Seq: total RNA was isolated from seedlings using QIAgen Plant RNeasy kit. PlaNET-Seq: NGS libraries were constructed from nascent RNA using Small RNA-Seq Kit v3 (Bioo Scientific). The original protocol was modified to incorporate alkaline RNA fragmentation step after 3' adapter ligation. RNA-Seq: polyA-enriched libraries were constructed using Illumina TruSeq RNA Sample Prep Kit v2. Illumina HiSeq 4000 gds 303900885 GSM3900885 GEO Accession GSM3900885 SRX6102436 GSM3900886 SRP202206 SRS5002892 GSM3900886 RNA-Seq TRANSCRIPTOMIC cDNA PlaNET-Seq: Nuclei were isolated from 3 grams of seedlings. Chromatin was solubilized by DNase I treatment. Nascent RNA fraction was enriched by immunoprecipitation of FLAG-tagged RNAPII elongation complexes using anti-FLAG antibody (F3165, Sigma-Aldrich) coupled to Dynabeads Protein G. Finally, RNAPII complexes were eluted from Dynabeads by 3xFLAG peptide, and the nascent RNA was purified using miRNeasy kit (QIAgen). RNA-Seq: total RNA was isolated from seedlings using QIAgen Plant RNeasy kit. PlaNET-Seq: NGS libraries were constructed from nascent RNA using Small RNA-Seq Kit v3 (Bioo Scientific). The original protocol was modified to incorporate alkaline RNA fragmentation step after 3' adapter ligation. RNA-Seq: polyA-enriched libraries were constructed using Illumina TruSeq RNA Sample Prep Kit v2. Illumina HiSeq 4000 gds 303900886 GSM3900886 GEO Accession GSM3900886