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)