Table 1: AtGenExpress - hormone and inhibitor treatments
No. Exp. Laboratory Control Genotype Treatment Time point Organ/Tissue growth condition Age Replicates Abbreviation

Basic hormone treatment of seedlings: Arabidopsis thaliana seedlings (genotypes Col-0, ga1-5, or det2-1) were grown in MS-liquid medium for 7 days at 23 ˚C and treated with IAA, zeatin, GA3, ABA, MJ, ACC, or BL for 30 min., 1 hour, or 3 hours.
1 A Shimada & Yoshida T Col-0 mock 30min seedling MS-liquid 7 d 2 mock 30m (A1)
2 A Shimada & Yoshida Col-0 1 µM IAA 30min seedling MS-liquid 7 d 2 IAA 30m (A1)
3 A Shimada & Yoshida Col-0 1 µM zeatin 30min seedling MS-liquid 7 d 2 Zeatin 30m (A1)
4 A Shimada & Yoshida Col-0 1 µM GA3 30min seedling MS-liquid 7 d 2 GA 30m (A1)
5 A Shimada & Yoshida Col-0 10 µM ABA 30min seedling MS-liquid 7 d 2 ABA 30m (A1)
6 A Shimada & Yoshida Col-0 10 µM MJ 30min seedling MS-liquid 7 d 2 MJ 30m (A1)
7 A Shimada & Yoshida Col-0 10 µM ACC 30min seedling MS-liquid 7 d 2 ACC 30m (A1)
8 A Shimada & Yoshida Col-0 10 nM BL 30min seedling MS-liquid 7 d 2 BL 30m (A1)
9 A Shimada & Yoshida T Col-0 mock 1h seedling MS-liquid 7 d 2 mock 1h (A2)
10 A Shimada & Yoshida Col-0 1 µM IAA 1h seedling MS-liquid 7 d 2 IAA 1h (A2)
11 A Shimada & Yoshida Col-0 1 µM zeatin 1h seedling MS-liquid 7 d 2 Zeatin 1h (A2)
12 A Shimada & Yoshida Col-0 1 µM GA3 1h seedling MS-liquid 7 d 2 GA 1h (A2)
13 A Shimada & Yoshida Col-0 10 µM ABA 1h seedling MS-liquid 7 d 2 ABA 1h (A2)
14 A Shimada & Yoshida Col-0 10 µM MJ 1h seedling MS-liquid 7 d 2 MJ 1h (A2)
15 A Shimada & Yoshida Col-0 10 µM ACC 1h seedling MS-liquid 7 d 2 ACC 1h (A2)
16 A Shimada & Yoshida Col-0 10 nM BL 1h seedling MS-liquid 7 d 2 BL 1h (A2)
17 A Shimada & Yoshida T Col-0 mock 3h seedling MS-liquid 7 d 2 mock 3h (A3)
18 A Shimada & Yoshida Col-0 1 µM IAA 3h seedling MS-liquid 7 d 2 IAA 3h (A3)
19 A Shimada & Yoshida Col-0 1 µM zeatin 3h seedling MS-liquid 7 d 2 Zeatin 3h (A3)
20 A Shimada & Yoshida Col-0 1 µM GA3 3h seedling MS-liquid 7 d 2 GA 3h (A3)
21 A Shimada & Yoshida Col-0 10 µM ABA 3h seedling MS-liquid 7 d 2 ABA 3h (A3)
22 A Shimada & Yoshida Col-0 10 µM MJ 3h seedling MS-liquid 7 d 2 MJ 3h (A3)
23 A Shimada & Yoshida Col-0 10 µM ACC 3h seedling MS-liquid 7 d 2 ACC 3h (A3)
24 A Shimada & Yoshida Col-0 10 nM BL 3h seedling MS-liquid 7 d 2 BL 3h (A3)
25 A Shimada & Yoshida T ga1-5 mock 30min seedling MS-liquid 7 d 2 ga1mock 30m (A4)
26 A Shimada & Yoshida ga1-5 1 µM GA3 30min seedling MS-liquid 7 d 2 ga1+GA 30m (A4)
27 A Shimada & Yoshida T ga1-5 mock 1h seedling MS-liquid 7 d 2 ga1mock 1h (A5)
28 A Shimada & Yoshida ga1-5 1 µM GA3 1h seedling MS-liquid 7 d 2 ga1+GA 1h (A5)
29 A Shimada & Yoshida T ga1-5 mock 3h seedling MS-liquid 7 d 2 ga1mock 3h (A6)
30 A Shimada & Yoshida ga1-5 1 µM GA3 3h seedling MS-liquid 7 d 2 ga1+GA 3h (A6)
31 A Shimada & Yoshida T det2-1 mock 30min seedling MS-liquid 7 d 2 det2mock 30m (A7)
32 A Shimada & Yoshida det2-1 10 nM BL 30min seedling MS-liquid 7 d 2 det2+BL 30m (A7)
33 A Shimada & Yoshida T det2-1 mock 1h seedling MS-liquid 7 d 2 det2mock 1h (A8)
34 A Shimada & Yoshida det2-1 10 nM BL 1h seedling MS-liquid 7 d 2 det2+BL 1h (A8)
35 A Shimada & Yoshida T det2-1 mock 3h seedling MS-liquid 7 d 2 det2mock 3h (A9)
36 A Shimada & Yoshida det2-1 10 nM BL 3h seedling MS-liquid 7 d 2 det2+BL 3h (A9)

Brassinosteroids treatment of seedlings: Arabidopsis thaliana seedlings (genotypes det2-1) were grown in MS-liquid medium for 7 days at 23 ˚C and were treated with campestanol, 6-deoxocathasterone, cathasterone, 6-deoxoteasterone, teasterone, 3-dehydro-6-deoxoteasterone, 3-dehydroteasterone, 6-deoxotyphasterol, typhasterol, 6-deoxocastasterone, castasterone, or brassinolide for 3 hours.
37 B Shimada & Yoshida T det2-1 mock 3h seedling MS-liquid 7 d 2 mock 3h (B)
38 B Shimada & Yoshida det2-1 10 µM campestanol 3h seedling MS-liquid 7 d 2 CN 3h (B)
39 B Shimada & Yoshida det2-1 1 µM 6-deoxocathasterone 3h seedling MS-liquid 7 d 2 6DCT 3h (B)
40 B Shimada & Yoshida det2-1 1 µM cathasterone 3h seedling MS-liquid 7 d 2 CT 3h (B)
41 B Shimada & Yoshida det2-1 1 µM 6-deoxoteasterone 3h seedling MS-liquid 7 d 2 6DTE 3h (B)
42 B Shimada & Yoshida det2-1 1 µM teasterone 3h seedling MS-liquid 7 d 2 TE 3h (B)
43 B Shimada & Yoshida det2-1 1 µM 3-dehydro-6-deoxoteasterone 3h seedling MS-liquid 7 d 2 6D3DT 3h (B)
44 B Shimada & Yoshida det2-1 1 µM 3-dehydroteasterone 3h seedling MS-liquid 7 d 2 3DT 3h (B)
45 B Shimada & Yoshida det2-1 1 µM 6-deoxotyphasterol 3h seedling MS-liquid 7 d 2 6DTY 3h (B)
46 B Shimada & Yoshida det2-1 1 µM typhasterol 3h seedling MS-liquid 7 d 2 TY 3h (B)
47 B Shimada & Yoshida det2-1 1 µM 6-deoxocastasterone 3h seedling MS-liquid 7 d 2 6DCS 3h (B)
48 B Shimada & Yoshida det2-1 100 nM castasterone 3h seedling MS-liquid 7 d 2 CS 3h (B)
49 B Shimada & Yoshida det2-1 10 nM brassinolide 3h seedling MS-liquid 7 d 2 BL 3h (B)

Cytokinin treatment of seedlings: Arabidopsis thaliana seedlings (genotypes Col-0, ARR22-ox) were grown on MS-agar plates for 21 days at 22 ˚C and were treated with t-zeatin for 3 hours.
50 C Sakakibara & Mizuno T Col-0 no treatment 0h seedling MS-agar 21 d 3 Cont (C1)
51 C Sakakibara & Mizuno Col-0 20 µM t-zeatin 3h seedling MS-agar 21 d 3 Zeatin20µM (C1)
52 C Sakakibara & Mizuno T ARR22-ox no treatment 0h seedling MS-agar 21 d 3 ARR22-ox (C2)
53 C Sakakibara & Mizuno ARR22-ox 20 µM t-zeatin 3h seedling MS-agar 21 d 3 ARR22-ox+Zeatin20µM (C2)

Effect of ABA during seed imbibition: Dry seeds of Arabidopsis thaliana (genotype Col-0) were imbibed in water or ABA solution for 24 h at 22 ˚C under continuous light.
54 D Nambara & Kamiya T Col-0 dry seeds 0h seeds N/A 0 d 2 Dry seed (D)
55 D Nambara & Kamiya T Col-0 imbibed seeds (water) 24h seeds N/A 0 d 2 Imbibed 24h (D)
56 D Nambara & Kamiya Col-0 imbibed seeds (3 µM ABA) 24h seeds N/A 0 d 2 Imbibed 24h+ABA3µM (D)
57 D Nambara & Kamiya Col-0 imbibed seeds (30 µM ABA) 24h seeds N/A 0 d 2 Imbibed 24h+ABA30µM (D)

Effect of gibberellin during seed imbibition: Seeds of Arabidopsis thaliana (genotype ga1-3) were grown in water for 24 hours with white light at 22 ˚C and treated with water or gibberellin solution.
58 E Yamaguchi & Kamiya T ga1-3 mock 3h seeds water 24 h 2 ga1-3 imbibed 3h (E1)
59 E Yamaguchi & Kamiya T ga1-3 mock 6h seeds water 24 h 2 ga1-3 imbibed 6h (E2)
60 E Yamaguchi & Kamiya T ga1-3 mock 9h seeds water 24 h 2 ga1-3 imbibed 9h (E3)
61 E Yamaguchi & Kamiya ga1-3 5 µM gibberellin 3h seeds water 24 h 2 ga1-3 imbibed 3h+GA (E1)
62 E Yamaguchi & Kamiya ga1-3 5 µM gibberellin 6h seeds water 24 h 2 ga1-3 imbibed 6h+GA (E2)
63 E Yamaguchi & Kamiya ga1-3 5 µM gibberellin 9h seeds water 24 h 2 ga1-3 imbibed 9h+GA (E3)

Effect of GA inhibitors on seedlings: Arabidopsis thaliana seedlings (genotype Col-0) were grown in MS-liquid medium for 7 days at 23 ˚C and were treated with propiconazole, uniconazole, paclobutrazol, or prohexadione for 3 or 12 hours.
64 F Shimada & Yoshida T Col-0 mock 3h seedling MS-liquid 7 d 2 mock 3h (F1)
65 F Shimada & Yoshida T Col-0 mock 12h seedling MS-liquid 7 d 2 mock 12h (F2)
66 F Shimada & Yoshida Col-0 10 µM propiconazole 3h seedling MS-liquid 7 d 2 PPI 3h (F1)
67 F Shimada & Yoshida Col-0 10 µM propiconazole 12h seedling MS-liquid 7 d 2 PPI 12h (F2)
68 F Shimada & Yoshida Col-0 10 µM uniconazole 3h seedling MS-liquid 7 d 2 Unic 3h (F1)
69 F Shimada & Yoshida Col-0 10 µM uniconazole 12h seedling MS-liquid 7 d 2 Unic 12h (F2)
70 F Shimada & Yoshida Col-0 10 µM paclobutrazol 3h seedling MS-liquid 7 d 2 Pac 3h (F1)
71 F Shimada & Yoshida Col-0 10 µM paclobutrazol 12h seedling MS-liquid 7 d 2 Pac 12h (F2)
72 F Shimada & Yoshida Col-0 10 µM prohexadione 3h seedling MS-liquid 7 d 2 PX 3h (F1)
73 F Shimada & Yoshida Col-0 10 µM prohexadione 12h seedling MS-liquid 7 d 2 PX 12h (F2)

Effect of auxin inhibitors on seedlings: Arabidopsis thaliana seedlings (genotype Col-0) were grown in MS-liquid medium for 7 days at 23 ˚C and were treated with 2,4,6-trihydroxybenzamide, p-chlorophenoxyisobutyric acid, 2,3,5-triiodobenzoic acid, or naphthylphthalamic acid for 3 hours.
74 F Shimada & Yoshida T Col-0 mock 3h seedling MS-liquid 7 d 2 mock 3h (F1)
75 F Shimada & Yoshida Col-0 10 µM 2,4,6T 3h seedling MS-liquid 7 d 2 246T 3h (F1)
76 F Shimada & Yoshida Col-0 10 µM PCIB 3h seedling MS-liquid 7 d 2 PCIB 3h (F1)
77 F Shimada & Yoshida Col-0 10 µM TIBA 3h seedling MS-liquid 7 d 2 TIBA 3h (F1)
78 F Shimada & Yoshida Col-0 10 µM NPA 3h seedling MS-liquid 7 d 2 NPA 3h (F1)

Effect of brassinosteroid inhibitors on seedlings: Arabidopsis thaliana seedlings (genotype Col-0) were grown in MS-liquid medium for 7 days at 23 ˚C and were treated with brassinazole 220 or brassinazole 91 for 3 or 12 hours.
79 F Shimada & Yoshida T Col-0 mock 3h seedling MS-liquid 7 d 2 mock 3h (F1)
80 F Shimada & Yoshida T Col-0 mock 12h seedling MS-liquid 7 d 2 mock 12h (F2)
81 F Shimada & Yoshida Col-0 10 µM Brz220 3h seedling MS-liquid 7 d 2 Brz220 10µM3h (F1)
82 F Shimada & Yoshida Col-0 10 µM Brz220 12h seedling MS-liquid 7 d 2 Brz220 10µM12h (F2)
83 F Shimada & Yoshida Col-0 10 µM Brz91 3h seedling MS-liquid 7 d 2 Brz91 3h (F1)
84 F Shimada & Yoshida Col-0 10 µM Brz91 12h seedling MS-liquid 7 d 2 Brz91 12h (F2)
85 G Shimada & Yoshida T Col-0 mock 3h seedling MS-liquid 7 d 2 mockBrz 3h (G)
86 G Shimada & Yoshida Col-0 3 µM Brz220 3h seedling MS-liquid 7 d 2 Brz220 3µM3h (G)

Effect of ethylene inhibitors on seedlings: Arabidopsis thaliana seedlings (genotype Col-0) were grown in MS-liquid medium for 7 days at 23 ˚C and were treated with AgNO3 or aminoethoxyvinylglycine for 3 hours.
87 F Shimada & Yoshida T Col-0 mock 3h seedling MS-liquid 7 d 2 mock 3h@(F1)
88 F Shimada & Yoshida Col-0 10 µM AgNO3 3h seedling MS-liquid 7 d 2 AgNO3 3h (F1)
89 F Shimada & Yoshida Col-0 10 µM AVG 3h seedling MS-liquid 7 d 2 AVG 3h (F1)

Effect of other inhibitors on seedlings: Arabidopsis thaliana seedlings (genotype Col-0) were grown in MS-liquid medium for 7 days at 23 ˚C and were treated with CHX (cycloheximide), MG132 (carbobenzoxyl-leucinyl-leucinyl-leucinal), PNO8 (N-octyl-3-nitro-2,4,6-trihydroxybenzamide), ibuprofen, daminozide, or salicylic acid for 3 or 12 hours.
90 F Shimada & Yoshida T Col-0 mock 3h seedlings MS-liquid 7 d 2 mock 3h (F1)
91 F Shimada & Yoshida Col-0 10 µM CHX 3h seedlings MS-liquid 7 d 2 CHX 3h (F1)
92 F Shimada & Yoshida Col-0 10 µM MG132 3h seedlings MS-liquid 7 d 2 MG132 3h (F1)
93 F Shimada & Yoshida T Col-0 mock 12h seedlings MS-liquid 7 d 2 mock 12h (F2)
94 F Shimada & Yoshida Col-0 1 µM PNO8 3h seedlings MS-liquid 7 d 2 PNO8 1µM3h (F1)
95 F Shimada & Yoshida Col-0 1 µM PNO8 12h seedlings MS-liquid 7 d 2 PNO8 1µM12h (F2)
96 G Shimada & Yoshida T Col-0 mock 3h seedlings MS-liquid 7 d 2 mockBrz 3h (G)
97 G Shimada & Yoshida Col-0 10 µM PNO8 3h seedlings MS-liquid 7 d 2 PNO8 10µM3h (G)
98 F Shimada & Yoshida Col-0 10 µM ibuprofen 3h seedlings MS-liquid 7 d 2 Ibup 3h (F1)
99 F Shimada & Yoshida Col-0 10 µM daminozide 3h seedlings MS-liquid 7 d 2 B9 3h (F1)
100 F Shimada & Yoshida Col-0 10µM salicylic acid 3h seedlings MS-liquid 7 d 2 Sal 3h (F1)


Table 2: AtGenExpress - various genotypes
No. Exp. Laboratory Control Genotype Treatment Time point Organ/Tissue growth condition Age Replicates Abbreviation

Comparison of plant hormone related mutant: Arabidopsis thaliana seedlings (genotypes Ws-2, bri1-5, Ler-1, ga1-5) were grown in MS-liquid medium for 7 days at 23 ˚C.
101 H Shimada & Yoshida T Ws-2 no treatment N/A seedling MS-liquid 7 d 2 WT-WS (H)
102 H Shimada & Yoshida bri1-5 no treatment N/A seedling MS-liquid 7 d 2 bri1 (H)
103 K Shimada & Yoshida T Ler-1 no treatment N/A seedling MS-liquid 7 d 2 WT-Ler (K)
104 K Shimada & Yoshida ga1-5 no treatment N/A seedling MS-liquid 7 d 2 ga1 (K)

ARR21C overexpression: Arabidopsis thaliana seedlings (genotypes Col-0, ARR21C-ox) were grown on MS-agar plates for 21 days at 22 ˚C.
105 L Sakakibara & Mizuno T Col-0 no treatment N/A seedling MS-agar 21 d 3 Cont (L)
106 L Sakakibara & Mizuno ARR21C-ox no treatment N/A seedling MS-agar 21 d 3 ARR21C-ox (L)


Table 3: AtGenExpress - development
No. Exp. Laboratory Control Genotype Treatment Time point Organ/Tissue growth condition Age Replicates Abbreviation

Time course of early seed germination: Dry seeds of Arabidopsis thaliana (genotype Col-0) were or imbibed in water for 1 h or 3 h at 22 ˚C under continuous light.
107 M Nambara & Kamiya T Col-0 no treatment 0h seeds N/A 0 d 2 Dry seed (M)
108 M Nambara & Kamiya Col-0 imbibed seeds (water) 1h seeds N/A 0 d 2 Imbibed 1h (M)
109 M Nambara & Kamiya Col-0 imbibed seeds (water) 3h seeds N/A 0 d 2 Imbibed 3h (M)


Table 4: AtGenExpress - abiotic treatments
No. Exp. Laboratory Control Genotype Treatment Time point Organ/Tissue growth condition Age Replicates Abbreviation

Different temperature treatment of seeds: Seeds of Arabidopsis thaliana (genotype Ler-0), were irradiated with a far-red light pulse 1 h after imbibition, then incubated for 96 hours in the dark at 22 ˚C or 4 ˚C.
110 N Yamaguchi & Kamiya T Ler-0 incubated at 22 ˚C 96h seeds N/A 0 d 2 Imbibed 96h22dg. (N)
111 N Yamaguchi & Kamiya Ler-0 incubated at 4 ˚C 96h seeds N/A 0 d 2 Imbibed 96h4dg. (N)

Response to sulfate limitation: Arabidopsis thaliana seedlings (genotype Col-0) were vertically grown for 10 days on MGRL-agar medium containing 1500 µM sulfate at 22 ˚C under 16 h/8 h light and dark cycles and than transferred to medium containing or lacking sulfate.
112 P Takahashi T Col-0 1500 µM sulfate 0h root MGRL-agar 10 d 2 +S 0h (P)
113 P Takahashi T Col-0 mock (1500 µM sulfate) 2h root MGRL-agar 10 d 2 +S 2h (P2)
114 P Takahashi T Col-0 mock (1500 µM sulfate) 4h root MGRL-agar 10 d 2 +S 4h (P3)
115 P Takahashi T Col-0 mock (1500 µM sulfate) 8h root MGRL-agar 10 d 2 +S 8h (P4)
116 P Takahashi T Col-0 mock (1500 µM sulfate) 12h root MGRL-agar 10 d 2 +S 12h (P5)
117 P Takahashi T Col-0 mock (1500 µM sulfate) 24h root MGRL-agar 10 d 2 +S 24h (P6)
118 P Takahashi Col-0 0 µM sulfate 2h root MGRL-agar 10 d 2 -S 2h (P2)
119 P Takahashi Col-0 0 µM sulfate 4h root MGRL-agar 10 d 2 -S 4h (P3)
120 P Takahashi Col-0 0 µM sulfate 8h root MGRL-agar 10 d 2 -S 8h (P4)
121 P Takahashi Col-0 0 µM sulfate 12h root MGRL-agar 10 d 2 -S 12h (P5)
122 P Takahashi Col-0 0 µM sulfate 24h root MGRL-agar 10 d 2 -S 24h (P6)