RNA-Seq of Col-0 replicate 2 Basecalls performed using CASAVA version 1.?Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.Genome_build: TAIR9
RNA-Seq of iaa3 replicate 1 Basecalls performed using CASAVA version 1.?Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.Genome_build: TAIR9
RNA-Seq of pifq;bzr1-1D replicate 1 Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.Genome Build:QB_L1.count.txt: Arabidopsis TAIR9
RNA-Seq of iaa3 replicate 2 Basecalls performed using CASAVA version 1.?Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.Genome_build: TAIR9
RNA-Seq of bzr1-1D replicate 2 Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.Genome Build:B_L2.count.txt: Arabidopsis TAIR9
Chromatin IP against ARF6 transcription factor ARF6 binding peaks were identified using ChIP-Seq analysis R (CSAR) software with parameters (backg=10, norm=-1, test="Ratio", times=1e6, digits=2) (Muino et al., 2011)Genome_build: TAIR9
replicate 2 Total reads were mapped to the Arabidopsis thaliana genome (TAIR10, www.arabidopsis.org) using TopHat v1.4.0, with parameters --min-segment-intron 40 --max-segment-intron 2000 --bowtie --no-novel-juncs --read-mismatches 2 -GRead counts for each gene were quantified using HTSeq-count with union mode.Genome_build: TAIR10, www.arabidopsis.orgSupplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
RNA-Seq of bzr1-1D replicate 2 Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.Genome Build:B_L2.count.txt: Arabidopsis TAIR9
RNA-Seq of Col-0 replicate 1 Basecalls performed using CASAVA version 1.?Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.Genome_build: TAIR9
RNA-Seq of pifq replicate 2 Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.Genome Build:Q_L2.count.txt: Arabidopsis TAIR9