REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-GFP polyclonal antibody	ChromoTek	RRID: AB_2749857
Chemicals, peptides, and recombinant proteins
GoTaq DNA Polymerase	Promega	Cat #M3001
Schiff reagent	Merck	1090330500
Renaissance 2200 staining	Renaissance Chemicals	https://www.renchem.co.uk/products/renaissance-SR-2200
miRCURY LNA miRNA Detection Probes	Qiagen	Cat # 339111 YD00612441-BCD
Critical commercial assays
SV Total RNA Isolation Kit	Promega	Cat #Z3101
Superscript II Reverse transcriptase	Invitrogen	Cat # 18064022
Real Mix qPCR	Biodynamics	Cat # A6101
iTaq SYBR green master mix	Bio-Rad	Cat#1725121
DIG RNA Labeling Kit (SP6/T7)	Roche	Cat#11175025910
Deposited data
Methylation raw sequence reads	this study	NCBI Database: PRJNA750614 https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA750614
Experimental models: Organisms/strains
Arabidopsis thaliana ARF10:mARF10-GFP line A	The Nottingham Arabidopsis Stock Centre (NASC)	N16288
Arabidopsis thaliana ARF10:mARF10-GFP line B	The Nottingham Arabidopsis Stock Centre (NASC)	N16289
Arabidopsis thaliana Col-0	The Nottingham Arabidopsis Stock Centre (NASC)
Arabidopsis thaliana pKNU::nlsYFP	Tucker et al.,31
Arabidopsis thaliana pLC2::nlsYFP	Tucker et al.,31
Arabidopsis thaliana ASY3::RFP	Yang et al.,32
Arabidopsis thaliana pWOX2::CENH3_GFP	De Storme et al.,33
Arabidopsis thaliana FGR7.0	Völz et al.,34
Arabidopsis thaliana arf10_2	The Nottingham Arabidopsis Stock Centre (NASC)	N655696
Arabidopsis thaliana arf10_3	The Nottingham Arabidopsis Stock Centre (NASC)	N587560
Arabidopsis thaliana stk-2	Pinyopich et al.,37
Arabidopsis thaliana ago1-27	Morel et al.,35
Oligonucleotides
Oligonucleotides for genotyping and expression analyses	See Table S4
Oligonucleotides for DNA methylation analysis	See Table S4
Oligonucleotides for Chromatin immunoprecipitation assay	See Table S4
Software and algorithms
Axiovision 4.1	Carl Zeiss AG	https://www.micro-shop.zeiss.com/it/ch/
LAS AF 2.2.0. A	Leica Microsystems Srl	https://www.leica-microsystems.com/
R version 3.3.2	R Core Team (2023)	www.r-project.org
Methylation Content Sensitive Enzyme Double-Digest Restriction-Site-Associated DNA (ddRAD) technique (MCSeEd)	Pipeline for methylation analysis from raw reads to DMR identification	https://bitbucket.org/capemaster/mcseed/src/master/
REST-RG 2009	QIAGEN	http://www.REST.de.com
QuantaSoft™	BioRad	https://www.bio-rad.com/en-it/SearchResults? Text=quantasoft