SRX5891249 GSM3814845 SRP199385 SRS4812971 GSM3814845 OTHER TRANSCRIPTOMIC other 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). TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). 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. TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). Illumina HiSeq 4000 gds 303814845 GSM3814845 GEO Accession GSM3814845 SRX5891250 GSM3814846 SRP199385 SRS4812972 GSM3814846 OTHER TRANSCRIPTOMIC other 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). TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). 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. TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). Illumina HiSeq 4000 gds 303814846 GSM3814846 GEO Accession GSM3814846 SRX5891251 GSM3814847 SRP199385 SRS4812973 GSM3814847 OTHER TRANSCRIPTOMIC other 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). TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). 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. TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). Illumina HiSeq 4000 gds 303814847 GSM3814847 GEO Accession GSM3814847 SRX5891252 GSM3814848 SRP199385 SRS4812974 GSM3814848 OTHER TRANSCRIPTOMIC other 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). TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). 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. TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). Illumina HiSeq 4000 gds 303814848 GSM3814848 GEO Accession GSM3814848 SRX5891253 GSM3814849 SRP199385 SRS4812975 GSM3814849 OTHER TRANSCRIPTOMIC other 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). TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). 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. TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). Illumina HiSeq 4000 gds 303814849 GSM3814849 GEO Accession GSM3814849 SRX5891254 GSM3814850 SRP199385 SRS4812976 GSM3814850 OTHER TRANSCRIPTOMIC other 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). TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). 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. TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). Illumina HiSeq 4000 gds 303814850 GSM3814850 GEO Accession GSM3814850 SRX5891257 GSM3814853 SRP199385 SRS4812979 GSM3814853 OTHER TRANSCRIPTOMIC other 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). TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). 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. TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). Illumina HiSeq 4000 gds 303814853 GSM3814853 GEO Accession GSM3814853 SRX5891258 GSM3814854 SRP199385 SRS4812980 GSM3814854 OTHER TRANSCRIPTOMIC other 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). TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). 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. TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). Illumina HiSeq 4000 gds 303814854 GSM3814854 GEO Accession GSM3814854 SRX5891259 GSM3814855 SRP199385 SRS4812981 GSM3814855 OTHER TRANSCRIPTOMIC other 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). TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). 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. TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). Illumina HiSeq 4000 gds 303814855 GSM3814855 GEO Accession GSM3814855 SRX5891260 GSM3814856 SRP199385 SRS4812982 GSM3814856 OTHER TRANSCRIPTOMIC other 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). TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). 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. TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). Illumina HiSeq 4000 gds 303814856 GSM3814856 GEO Accession GSM3814856 SRX5891261 GSM3814857 SRP199385 SRS4812983 GSM3814857 OTHER TRANSCRIPTOMIC other 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). TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). 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. TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). Illumina HiSeq 4000 gds 303814857 GSM3814857 GEO Accession GSM3814857 SRX5891262 GSM3814858 SRP199385 SRS4812984 GSM3814858 OTHER TRANSCRIPTOMIC other 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). TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). 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. TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). NextSeq 500 gds 303814858 GSM3814858 SRX5891263 GSM3814859 SRP199385 SRS4812985 GSM3814859 OTHER TRANSCRIPTOMIC other 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). TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). 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. TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695). NextSeq 500 gds 303814859 GSM3814859