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. Author manuscript; available in PMC: 2022 Sep 13.
Published in final edited form as: Dev Cell. 2021 Aug 17;56(17):2501–2515.e5. doi: 10.1016/j.devcel.2021.07.016
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
anti-Actin antibody (rabbit) Millipore-Sigma Cat#SAB4301137
anti-ATG5 antibody (rabbit) Agrisera Cat#AS15 3060
anti-ATG8a antibody (rabbit) Abcam Cat#ab77003
Bacterial and virus strains
Agrobacterium tumefaciens Widely distributed Strain GV3101
Chemicals, peptides, and recombinant proteins
3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) Sigma-Aldrich Cat#D2425
5-bromo-4-chloro-3-indolyl-beta-D-glucuronic acid, cyclohexylammonium salt (X-gluc) Thermo Fisher Scientific Cat#R0851
Agar AmericanBio Cat#AB01185
cOmplete EDTA-free Protease Inhibitor Cocktail Roche Cat#11873580001
D-luciferin Cayman Chemical Company Cat#115144-35-9
Murashige & Skoog Basal Medium (MS) Cassion Laboratories Cat#MSP01
Murashige & Skoog Basal Medium without nitrogen PhytoTech Labs Cat#M531
Phenylmethylsulfonyl fluoride (PMSF) AmericanBio Cat#AB01620-00005
TRIzol™ Thermo Fisher Scientific Cat#15596026
Critical commercial assays
iScript™ Reverse Transcription Supermix Bio-Rad Cat#1708841
iTaq Universal SYBR Green Supermix Bio-Rad Cat#1725121
LR Clonase II Invitrogen Cat#11791020
Pierce™ BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225
RNeasy Plant Mini kit Qiagen Cat#74904
RNase-Free DNase Set Qiagen Cat#79254
Sucrose/D-Fructose/D-Glucose Assay Kit Megazyme Cat#K-SUFRG
TOPO cloning kit Invitrogen Cat#K240020
Total Starch Assay Kit Megazyme Cat#K-TSHK
Deposited data
Arabidopsis genome annotation TAIR10 www.arabidopsis.org
Microarray “longday” and “shortday” datasets (Michael, et al., 2008b) E-MEXP-1304
Microarray “LER_SD” dataset (Michael, et al., 2008a) E-MEXP-1299
Time course microarray data DIURNAL Project diurnal.mocklerlab.org
Experimental models: Organisms/strains
Arabidopsis thaliana: Col-0 wild type Widely distributed N/A
Arabidopsis: pp2-a13-1 ABRC SALK_101611
Arabidopsis: pgm-1 ABRC CS210
Arabidopsis: sex1-1 ABRC CS3093
Arabidopsis: co-9 ABRC CS870084
Arabidopsis: atg5-1 ABRC CS39993
Arabidopsis: atg7-2 ABRC CS69859
Arabidopsis: elf3-1 (Nusinow, et al., 2011) N/A
Arabidopsis: lux-4 (Nusinow, et al., 2011) N/A
Arabidopsis: PP2-A13promoter::Luciferase This paper N/A
Arabidopsis: PP2-A13promoter::gPP2-A13 in pp2-a13-1 This paper N/A
Arabidopsis: atg5-1 pp2-a13-1 This paper N/A
Arabidopsis: atg7-2 pp2-a13-1 This paper N/A
Arabidopsis: pgm-1 pp2-a13-1 This paper N/A
Arabidopsis: PP2-A13promoter::Luciferase in co-9 This paper N/A
Arabidopsis: PP2-A13promoter::Luciferase in pgm-1 This paper N/A
Arabidopsis: PP2-A13promoter::Luciferase in sex1-1 This paper N/A
Arabidopsis: PP2-A13promoter::Luciferase in elf3-1 This paper N/A
Arabidopsis: PP2-A13promoter::Luciferase in lux-4 This paper N/A
Oligonucleotides
See Table S5 This paper N/A
Recombinant DNA
Plasmid: pENTR-D-TOPO Thermo Fisher Scientific Cat#K240020
Plasmid: pFlash (Gendron, et al., 2012) N/A
Plasmid: pGWB16 (Nakagawa, et al., 2007) N/A
Plasmid: pMDC164 (Curtis and Grossniklaus, 2003) N/A
Plasmid: pSAT6-mCherry-VirD2NLS (Citovsky, et al., 2006) CD3-1106
Plasmid: pENTR- PP2-A13promoter (genomic) This paper N/A
Plasmid: pFlash-PP2-A13promoter::Luciferase (genomic) This paper N/A
Plasmid: pGWB16-PP2-A13promoter::gPP2-A13-4XMYC (genomic) This paper N/A
Plasmid: 35S::PP2-A13-GFP (cDNA) This paper N/A
Plasmid: pMDC164- A13promoter::GUS (genomic) This paper N/A
Software and algorithms
Code used is attached to this paper This paper N/A
Fiji (Schindelin, et al., 2012) imagej.net/software/fiji
ImageJ (Schneider, et al., 2012) imagej.nih.gov/ij
ggplot2 R package (Wickham, 2009) N/A
ggpubr R package (Kassambara, 2020) N/A
PRISM 8 GraphPad www.graphpad.com
Python (3.8.3) Python Software Foundation N/A
R(4.0.1) The R Project for Statistical Computing N/A
HHS Vulnerability Disclosure