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Flower Leaf Root Seed Seedlings, leaves and inflorescences Shoot Whole plant

1 day old_seed 1-5 days old_leaf 1-5 days old_whole 2 days old_seed 3 days old_root 3 days old_seed 3 days old_shoot 4 days old_seed 4 days old_seedling 4dpi_root 5 day post-fertilization_leaf 5 days old_root 5 days old_seed 5 days old_seedling 5 days old_shoot 5-10 days old_whole 5-week-old inflorescence and leaf tissues and 2-week-old seedlings 6 days after pollination_seed 6 days old_leaf 6 days old_seed 7 days old_leaf 7 days old_root 7 days old_seed 7 days old_seedling 8 days old_root 8 days old_seed 8 days old_seedling 8 days old_shoot 9 days old_root 9 days old_seed 10 days old_leaf 10 days old_root 10 days old_seedling 10 days old_shoot 11 days old_seedling 11-15 days old_whole 12 days old_seedling 13 days old_root 13 days old_seedling 14 days old_callus 14 days old_leaf 14 days old_root 14 days old_seed 14 days old_seedling 14 days old_shoot 15 days old_root 15 days old_seedling 15 days old_shoot 16 days old_shoot 16-20 days old_whole 17 days old_flower 17 days old_root 17-18 days old_root 18 days old_leaf 20 days old_leaf 20 days old_root 20 days old_seedling 20 days old_shoot 20 leaf stage 21 days old_flower 21 days old_leaf 21 days old_root 21 days old_seedling 21-25 days old_whole 21-35 days old_seedling 22 days old_seedling 25 days old_leaf 25 days old_root 26-30 days old_whole 27 days old_leaf 28 days old_cells 28 days old_flower 28 days old_leaf 28 days old_seedling 28 days old_shoot 28-35 days old_leaf 30 days old_leaf 35 days old_flower 35 days old_leaf 35 days old_root 35 days old_seedling 35 days old_shoot 35-42 days old_leaf 40 days old_leaf 42 days old_flower 42 days old_leaf 42 days old_root 42-56 days old_leaf 45 days old_leaf 45 days old_shoot 49 days old_leaf 49 days old_seed 49 days old_seedling 56 days old_seed 60 days old_leaf After ripening_seed Before bolting_leaf Bent cotyledon embryos Bicellular_pollen Bolting_leaf Bolting_shoot Bolting_whole Delayed flowering Dry seed Early heart embryos Early senescence_leaf Early torpedo embryos First flower opening_leaf FL.02 1/2 of flowers open stage Flowering stage_seed Flowering stage_shoot Freshly harvested_seed Germinating seed Globular embryos Late heart embryos Late senescence_leaf Late torpedo embryos LP.06 six Leaf visible Mature green embryos Mature_leaf Mature_pollen Mature_shoot Mature_whole Mixed stage_flower Preglobular embryos (8-cell/16-cell) Rosette_leaf Rosette_root Seedling Seedling_leaf Seedling_root Stage 1-12_flower Stage 1-12_leaf Stage 1-12_whole Stage 5_leaf Tricellular_pollen Two leaf stage Two leaf stage_seedling Unicellular Unopened floral bud Vegetative_root Vegetative_shoot Young_flower Young_leaf

1 µM epibrassinolide (epiBL) for 90 min 2 hours of 5 mM KNO3 5µM thermospermine 430 ± 50ppm CO2 concentration 810 ± 50ppm CO2 concentration ABA medium affinity-purified FLAG-AGO1 affinity-purified FLAG-AGO2 affinity-purified FLAG-AGO3 affinity-purified FLAG-AGO4 Air Alternaria brassicicola As(III) Botrytis cinerea Brassinosteroid Carbon deficiency Cold Control Copper deficiency Copper excess Cucumber Mosaic Virus Cuscuta pentagona Dark DEX treatment Drought Ethylene for 4hrs Flg22 Flg22/UV-B Heat Heterodera schachtii Hyaloperonospora arabidopsidis Iron deficiency Iron excess Jasmonate (JA) Light Low nitrate LS+As(III) Mannitol Meloidogyne javanica Methyl Jasmonate Mock MS medium Nitrogen deficiency Norflurazon Oilseed Rape Mosaic Virus Osmotic Oxygen deficiency Phosphate deficient Phosphate sufficient Phytophthora capsici Pseudomonas syringae Ralstonia solanacearum Room temperature Salt Salt/submergence Sclerotinia sclerotiorum Sound 10KHz/Ralstonia solanacearum Stratification Submergence Sulfur deficiency Tobacco Mosaic Virus Tobacco Rattle Virus Total lysate Turnip Crinkle Virus Turnip Mosaic Virus Turnip vein-clearing virus TuYVs81 UV

(23b6/35S-RTL1#11T1) / 3ab 4x Col 4x nrpd1a (Col) 5a 35S-RICE1 D52A 35S:AtAMT1;1 transgenic aar2-1 abh1-1 Additional point mutation in RDR6-tt19-8 background ago1 ago1-3 ago1-3 FLAG-AGO1D762A ago1-3 FLAG-AGO1E803A ago1-3 FLAG-AGO1H988F ago1-3/+ FLAG-AGO1D762A ago1-11 ago1-18 ago1-27 ago1-36 ago1-42 ago1hen1 AGO1sup19 ago2-1 ago2-1;PAGO2-HF-AGO2 ago3-2;PAGO3-FM-AGO3 ago4 ago4 dcl2/3/4 ago4-1 ago4-4 ago4-4/6-2/9-1 ago4-4/6-2/9-1/AGO4-D742A ago4-4/6-2/9-1/wtAGO4 ago4-4/AGO4-D742A ago4-4/wtAGO4 ago6 AGO10 OE AGO10 OE 4mAGO1 AGO10 overexpression aly1-2 amiR-PAG1 amiR-SUL amiR-SUL snc1-1 amiR-SUL sup-B65 aos arid2-/-arid3-/-arid4-/- arp6 knock out At-CHS silenced AtPAP2- atxr atxr5,6 cbp20 cbp80 cbp80_atxr cdc5-1 CDF2 clasy1 clf-29 lhp1-4 clsy1-7 clsy1-7,2-1 clsy1-7,2-1,3-1,4-1 clsy1-7,2-2 clsy1-7,2-2,3-1,4-1 clsy1-7,3-1 clsy1-7,4-1 clsy1-10 clsy2-1 clsy2-2 clsy2-2,3-1 clsy2-2,4-1 clsy3-1 clsy3-1,4-1 clsy3-2 clsy3-2,4-2 clsy4-1 clsy4-2 cmt2-7 cmt3-11 coi1 Col-0 Col-0 female X Cvi male Col-0 female X Ler male Col female x Col male Col female x Ler male ColxLer cpr1 aba1 crh6-3 (eco. Columbia) crt1-4 (eco. Columbia) Cvi female X Col-0 male Cvi female X Cvi male DCL1 homozygous DCL1 mutant dcl1-7 dcl2 dcl2-1 dcl2-1/dcl4-2 dcl2/3 dcl2/3/4 dcl2/4 dcl2/dcl4 dcl3 dcl3/4 dcl3/nrpd1 dcl3/rdr2 dcl4 rdr6 (Col) dcl4-2 dcl4-2 expressing cytosplasmic DCL4 from Ubq10 promoter dcl4-2 expressing nuclear DCL4 from Ubq10 promoter dcl4-2 rdr6-11 double dcl 234 nrpd1 dcp2 dcp2 and rdr6 double DDB2-FLAG ddc ddl-1 ddm1 ddm1 pol IV ddm1 pol IV rdr6 ddm1 pol V ddm1 rdr2 ddm1 rdr6 ddm1-2 ddm1-2 +/- ddm1-2 rdr6-15 ddm1-ago6 ddm1-dcl3 ddm1-pol4-rdr6 ddm1_2 dcl1_11 defected in RNA Polymerase II-transcribed trigger for generating silencing siRNA for RdDM, which is also defected in RNA Polymerase IV-dependent RdDM defected in RNA polymerase II-transcribed trigger for generating silencing siRNA for RdDM, which still partially silences the Target (T) locus defected in RNA polymerase II-transcribed trigger for generating silencing siRNA for RdDM, without the Target (T) locus DG14 dms3-1 dms4-1 drb1-1 drb2-1 double drb1-1 drb4-1 double drb1-1 single drb2-1 drb2-1 drb4-1 double drb2-1 single drb3-1 drb5-1 double drb4 drb4-1 drb4-1 single drb7.2 drd1-1 drm1-2,2-2 drm1/2 drm2-2 drm3-1 dtf1 dxo1-2 ein5-1 ski2-3 ein5-6 ein5-6 abh1-1 Empty vector control epcr1-/-epcr2-/- farnasyltransferase beta deletion frg1 to frg5 frg1/2 HA-AGO1-DAH HA-AGO1-DAH(ago2-1) HA-AGO2-DAD(ago2-1) HA-AGO10-DAH(ago2-1) HA-AGO10-DDH had-/- hda6-/- hen1-1 hen1-2 hen1-2/heso1-2 hen1-2/heso1-2/urt1-3 hen1-8 hen1-8 heso1-1 hen1-8 mee44 hen1-8 ntp2-1 hen1-8 ntp4-1 hen1-8 ntp5-1 hen1-8 ntp6-1 hen1-8 ntp7-1 hen1-8 ntp8-1 hen1-8 ntp10-1 hen1-8 urt1-1 hen1-9/heso1-1 heso-1-2 heso1-1 heso1-1/hen1-8 heso1-2/utr1-3 His-FLAG-AGO10 transgenic hyl1 hyl1-2 hyl1-2_hen2-4 hyl1-2_sop1-5 hyl1_atxr ilp1 ablation IWR1-type transcription factor , dms4 iyo-4 J2/J3 deletion, with transgenic J3C417S J2/J3 deletion, with transgenic wt J3 jmj14-1 jmj14-1 ldl1-2 ldl2 ldl1-2 ldl2 Ler female x 4N Col male Ler female x 4N Col nrpd1 male Ler female X Col-0 male Ler female X Ler male Ler female x Ler male Ler x Col mac7-1 met1 met1-3 MET1-3wt miR472OE miR1507 overexpression miR2109 overexpression miR2188a overexpression miR2188b overexpression miR2188c overexpression MSH1 +/+ msh1 -/- S1 msh1 -/- S2 nrp(d/e)2 nrpb/d/e11-1 nrpb2 nrpd1 nrpd1-3 nrpd1-4 nrpd1a nrpd1a (Col) nrpd1a (Salk_583051) nrpd1a-3 nrpd1a-4 (PolIV ) nrpd1a-4 (Pol IV) nrpd1b-1 (Pol V) nrpd1nrpe1 double NRPD1_ZF nrpe1-/- nrpe1-11 nrpe1-12 overexpressing RPL18 Overexpression line 7 Overexpression line 21 pAGO1:HA-AGO1 pAP1:AP1:GR ap1 cal parg1-1 parp1parp2 pistillata (Ler) x 4x Col pistillata (Ler) x 4x nrpd1a (Col) pistillata (Ler) x nrpd1a (Col) pkl-1 pLAT52::DsRed pMGH3::RTL1-Myc pol4 pol IV pol IV rdr6 pol V pp4r3a-1 pp4r3a-2 prl1prl2 ProAtUBQ10:AtAMT1;1-ORF transgenic PSR2-5 qqt2-2 rack1abc rdd rdm1-4 rdr/1/2/6 rdr1 rdr1/2/6 rdr2 rdr2 dcl2/3/4 rdr2-1 rdr6 rdr6-11 rdr6-11 ein5-1 ski2-3 rdr6-15 ros1 ros1/nrpd1 double RPF2-nad6 rrp6l1 rrp6l1-2 RTL1 with 35S promoter RTL1 with 35S promoter and dcl2 dcl3 dcl4 triple rtl2 RTL2 with 35S promoter RTL2 with 35S promoter and dcl2 dcl3 dcl4 triple sac3b-3 (SALK 065672) sac3b-7 (SALK 111245) sde4-3 sdn1 sdn2 AGO10 OE se se_atxr shh1-1 shh1-1 w/ shh1-3XMYC (D141A point ) shh1-1 w/ shh1-3XMYC (F162AF165A point ) shh1-1 w/ shh1-3XMYC (wild-type protein) shh1-1 w/ shh1-3XMYC (Y140A point ) shh1-1 w/ shh1-3XMYC (Y212A point ) shh1-1,clsy1-7,2-1 shh1-1,clsy1-7_ shh1-1,clsy3-1,4-1 shy43 SKI2 SKI2 and RDR6 sma1-1 smc4 snrk2.2/3/6 sov (aka Col-0) spo11-1-1 spt5l-1 stv-1 suvh2 suvh9 suvh4,5,6 suvr2 T-DNA insertion in TT19 (AT5G17220) under Col-0 background tgh-1 top1a-2 transgenic 35S::MIR164AC24 transgenic 35S::MIR164ACol-0 triple homozygous with dcl2-1, dcl3-1, dcl4-2t alleles urt1 (Salk_087647C) vcs (vcs-7 [SOV-L.er]) vcs-6 vcs-6 and rdr6 double vcs sov (aka vcs-7) VCS SOV (Col-0 [SOV-L.er]) WT xrn3-8