REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Gamborg B-5 basal medium	Phyto Technology	Cat#G398
Sucrose	ABCONE	Cat#57501
2-(N-morpholino) ethanesulfonic acid (MES)	BBI Life Sciences	Cat#145224948
Phytagel	Sigma-Aldrich	Cat#7101052-1
Agar Bacteriological Grade	Shanghai Jiafeng	Cat#H8145
Triton X-100	Sigma-Aldrich	Cat#9002931
KCl	Sigma-Aldrich	Cat#7447407
NaCl	Sigma-Aldrich	Cat#7647145
MgCl2·6H2O	Sigma-Aldrich	Cat#7791186
Tris base	Sigma-Aldrich	Cat#77861
DAPI	AAT Bioquest	Cat#28718903
2-Mercaptoethanol	Ruibio	Cat#60242
Spermine	Sigma-Aldrich	Cat#85590
Eva green dye	Biotium	Cat#31000
Phusion high-fidelity DNA polymerase	Thermo Fisher Scientific	Cat#022021
Complete protease inhibitor cocktail	Merck	Cat#04693132001
Critical commercial assays
MinElute Reaction Cleanup Kit	QIAGEN	Cat#28204
TruePrep DNA Library Prep Kit v2	Vazyme Biotech	Cat#TD50102
TruePrep Index Kit v2	Vazyme Biotech	Cat#TD202
2× NEBNext high-fidelity PCR mix	New England Biolabs	Cat#M0541L
AMPure beads	Beckman	Cat#A63880
Deposited data
ATAC-seq, ChIP-seq, and RNA-seq experiment data	This paper	BioProject PRJCA002620, Beijing Institute of Genomics Data Center (http://bigd.big.ac.cn)
Experimental models: organisms/strains
A. thaliana: Col-0	N/A	N/A
Software and algorithms
R version 3.6	The R Foundation	RRID: SCR_001905 https://www.r-project.orgl
Adobe Photoshop CC 2018	Adobe Acrobat	N/A
Adobe Illustrator CC 2018	Adobe Acrobat	N/A
Fastp	(Chen et al., 2018)	RRID: SCR_016962 https://github.com/OpenGene/fastp
FastQC v0.11.7	FastQC	RRID:SCR_014583 http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
MulitQC v1.6	(Ewels et al., 2016)	https://multiqc.info/
Bowtie2 v2.3.4.3	(Langmead and Salzberg, 2012)	http://bowtie-bio.sourceforge.net/bowtie2/
Samtools v1.9	(Li et al., 2009)	RRID: SCR_002105 http://www.htslib.org/
sambamba v0.6.7	(Tarasov et al., 2015)	https://lomereiter.github.io/sambamba/
bedtools v2.25.0	(Quinlan and Hall, 2010)	RRID: SCR_006646 https://bedtools.readthedocs.io/en/latest/
deepTools v3.1.2	(Ramirez et al., 2014)	RRID: SCR_016366 https://deeptools.readthedocs.io/en/develop/
featureCounts v1.6.2	(Liao et al., 2014)	RRID: SCR_012919 http://bioinf.wehi.edu.au/featureCounts/
DESeq2 v1.26.0	(Love et al., 2014)	RRID: SCR_015687 https://bioconductor.org/packages/release/bioc/html/DESeq2.html
MACS2 v2.1.2	(Zhang et al., 2008)	https://github.com/taoliu/MACS
DiffBind v2.14.0	(Ross-Innes et al., 2012)	RRID: SCR_012918 https://bioconductor.org/packages/release/bioc/html/DiffBind.html
ChIPseeker v1.22.0	(Yu et al., 2015)	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html
HOMER v4.10	(Heinz et al., 2010)	RRID: SCR_010881 http://homer.ucsd.edu/homer/
Intervene v0.6.1	(Khan and Mathelier, 2017)	https://intervene.readthedocs.io/en/latest/
Integrative Genomics Viewer	(Robinson et al., 2011)	RRID: SCR_011793 http://software.broadinstitute.org/software/igv/
Other
Eppendorf realplex2	Eppendorf	Cat#A248709R
The BD FACSAria II	BD	N/A
Percival chamber	Percival	N/A