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 |