Reagent/Resource	Reference or Source	Identifier or Catalog Number
Experimental Models
Arabidopsis thaliana dog1‐3	Nottingham Arabidopsis Stock Centre (NASC)	SALK_000867
Arabidopsis thaliana dog1‐5	Nottingham Arabidopsis Stock Centre (NASC)	SALK_022748
Arabidopsis thaliana puppies‐1	Nottingham Arabidopsis Stock Centre (NASC)	SALK_139540C
pDOG1‐LUC::DOG1	Fedak et al (2016)	N/A
psDOG1::LUC	Fedak et al (2016)	N/A
Oligonucleotides and sequence‐based reagents
Oligonucleotides	This study	Table EV3
Recombinant DNA
pHEE2E‐TRI	Jin & Marquardt (2020)	Addgene Plasmid #71288
pKI1.1R	Jin & Marquardt (2020)	Addgene Plasmid #85808
pMOD_A0402	Čermák et al (2017)	Addgene Plasmid #91009
pMOD_B2303	Čermák et al (2017)	Addgene Plasmid #91068
pMOD_C3001	Čermák et al (2017)	Addgene Plasmid #91094
pTRANS_230	Čermák et al (2017)	Addgene Plasmid #91118
Chemicals, enzymes and other reagents
Acidic phenol‐chloroform‐isoamyl alcohol 125:24:1 pH 4.5	ThermoFisher	AM9720
AGAROSE	BioShop	AGA001.1
Agencourt AMPure XP	Beckman Coulter	A63881
Agencourt AMPure XP magnetic beads	Beckman Coulter	A63881
All oligonucleotides (except stated otherwise)	Sigma‐Aldrich	N/A
Beetle luciferin potassium salt	Promega	E1605
Beta‐mercaptoethanol	Sigma‐Aldrich	M6250‐100ML
Betaine 5M	Sigma‐Aldrich	B0300‐1VL
Chloroform	POCH	234431116
CloneJET PCR Cloning Kit	ThermoFisher	K1232
COmplete protease inhibitors	Roche	5056489001
DAPI	Sigma‐Aldrich	D9564‐10MG
Dextran T40	Sigma‐Aldrich	31389‐500G
dNTP Mix 10 mM	ThermoFisher	R0192
DTT	ThermoFisher	DTT001.10
E. coli DNA Ligase	New England Biolabs	M0205L
E. coli DNA polymerase	New England Biolabs	M0209L
EDTA Sterile Solution 0.5 M pH 8.0	BioShop	EDT111.500
Empigen	Sigma‐Aldrich	30326‐50ML
Ethanol 96 %	POCH	396420113
Ficoll 400	BioShop	FIC400.100
Formaldehyde	Sigma‐Aldrich	F8775‐4x25ML
Formamide	POCH	432200116
Glufosinate ammonium	Sigma‐Aldrich	45520‐100MG
Glycerol	Chempur	114433204
HEPES	ACROS	FSBP31010
Hygromycin	BioShop	HYG002
Isopropanol	POCH	751500111
KCl	POCH	739740114
KH2PO4	Sigma‐Aldrich	P5655‐100G
Mannitol	BioShop	MAN509.500
Methanol	Chempur	603‐001‐00‐X
MgCl2	ThermoFisher	F 530‐S
Miracloth	Sigma‐Aldrich	475855‐1R
Murashige and Skoog (MS) medium	Sigma‐Aldrich	M0404‐10L
Murine RNase inhibitors	New England Biolabs	M0314L
N,N‐Dimethylformamide	Sigma‐Aldrich	227056‐250ML
Na2HPO4·7H2O	Sigma‐Aldrich	30413‐500G
NaCl	POCH	794121116
NEBNext Second Strand Synthesis (dNTP‐free) Reaction Buffer	New England Biolabs	B6117S
NP‐40	BioShop	NON505.100
Oligo(dT)	Sigma‐Aldrich	N/A
PEG 6000	Sigma‐Aldrich	8.07491.1000
PEG 8000 50%	New England Biolabs	M0242S
Percoll	Sigma‐Aldrich	P1644
Phenol equilibrated stabilized	Applichem	A1153,0100
Phusion High‐Fidelity DNA Polymerase	ThermoFisher	F 530‐S
Phusion High‐Fidelity HF Buffer	ThermoFisher	F 530‐S
Plant Agar	Duchefa	P1001.1000
PMSF	Sigma‐Aldrich	93482‐50ML‐F
Q5 Hot Start High‐Fidelity 2X Master Mix	New England Biolabs	M0049S
Qubit dsDNA HS	LifeTechnololies	Q32854
Random hexamers	ThermoFisher	N8080127
RiboLock 40 U/μl	ThermoFisher	EO0381
RNase H	New England Biolabs	M0297‐S
SDS	BDH Prolabo	444464T
Sodium acetate	POCH	805640115
Spectinomycin	BioShop	SPE201.5
Sucrose	CHEMPUR	117720907
SuperScript II	ThermoFisher	18064014
SuperScript III	ThermoFisher	18064014
SYBR Green mix	Roche	4887352001
T4 RNA ligase 2 Truncated 200 U/μl	New England Biolabs	M0242S
TRIS 1 M pH 7.5	Bioshop	TRS111
TRIS 1 M pH 8.0	Bioshop	TRS222
TRIS 1 M pH 8.5	Bioshop	TRS333
Triton X‐100	BioShop	TRX777.500
TSO oligo	FUTURE Synthesis	N/A
TURBO DNase kit	Ambion	AM1907
Urea	BioShop	URE001.500
Software
PartSeg	Bokota et al (2021)	N/A
Olympus xCellence Software	Olympus	N/A
Napari	Sofroniew et al (2022)	N/A
ImageJ	https://imagej.nih.gov/ij/download.html	N/A