Data Presentation for the 26k Microarray Project

table S1. Microarray data analysis using a linear model. Each experiment consisted of four dye-swaps and eight slides as described in the Methods and shown below. The analyzed data can be viewed in a “scatter plot” or “text”.

Experiment 1	At4 vs. Aa (leaves)	Common Variance (Plot, Text)	Per-gene Variance (Plot, Text)	Shared Gene List (Text)
Experiment 2	Allo733 vs. PM (leaves)	Common Variance (Plot, Text)	Per-gene Variance (Plot, Text)	Shared Gene List (Text)
Experiment 3	Allo738 vs. PM (leaves)	Common Variance (Plot, Text)	Per-gene Variance (Plot, Text)	Shared Gene List (Text)
Experiment 4	Allo733 vs. PM (flower buds)	Common Variance (Plot, Text)	Per-gene Variance (Plot, Text)	Shared Gene List (Text)
Experiment 5	Allo738 vs. PM (flower buds)	Common Variance (Plot, Text)	Per-gene Variance (Plot, Text)	Shared Gene List (Text)
Experiment 6	At2 vs. At4 (leaves)	Common Variance (Plot, Text)	Per-gene Variance (Plot, Text)	Shared Gene List (Text)

Notes.

1. In each experiment, a text-delineated table of the significant genes detected is displayed. For example, in experiment 1 for the comparison of gene expression between A. thaliana and A. arenosa in leaves, the list included 4,363 and 11,199 significant genes using common and per-gene variance, respectively. The list was tabulated using locus ID and logarithm-fold changes.

2. The microarray data were generated using procedures provided by MIAME (http://www.mged.org/Workgroups/MIAME/miame.html). The data were obtained from five experiments as shown below. The detailed procedures for microarray and experimental design, slide printing, hybridization, targets (cDNA probes), data collection, and analysis were described in a previous paper ¹⁹. The data can be down-loaded for re-analysis or verification of data analysis using other statistical packages or commercial software in addition to the linear model used in this study.

3. Raw data (spot quantitation matrix) were generated using a GenePix 4000B scanner and GenePix Pro4.1 software (Axon Instruments). The data obtained from each slide will be displayed after clicking the slide number.

4. The raw data (hybridization intensities obtained in Cy3 and Cy5 channels) were converted using the logarithm function and subjected to analysis of variance (ANOVA) as described in the Methods section. No additional step of data processing was used.

table S2. Microarray experimental design

table S2a. Microarray analysis of gene expression in leaves between two parents, A. thaliana (At4) and A. arenosa (Aa).

Slide No.	Leaf RNA	Cy3	Cy5	Printing Pattern	Dye-swap
1	RNA1	At4	Aa	1	1
2	RNA1	Aa	At4	1	1
3	RNA1	At4	Aa	2	2
4	RNA1	Aa	At4	2	2
5	RNA2	At4	Aa	1	3
6	RNA2	Aa	At4	1	3
7	RNA2	At4	Aa	2	4
8	RNA2	Aa	At4	2	4

table S2b. Microarray analysis of gene expression in leaves between Allo733 and parental mix.

Slide No.	Leaf RNA	Cy3	Cy5	Printing Pattern	Dye-swap
9	RNA1	Allo733	PM	1	1
10	RNA1	PM	Allo733	1	1
11	RNA1	Allo733	PM	2	2
12	RNA1	PM	Allo733	2	2
13	RNA2	Allo733	PM	1	3
14	RNA2	PM	Allo733	1	3
15	RNA2	Allo733	PM	2	4
16	RNA2	PM	Allo733	2	4

table S2c. Microarray analysis of gene expression in leaves between Allo738 and parental mix.

Slide No.	Leaf RNA	Cy3	Cy5	Printing Pattern	Dye-swap
17	RNA1	Allo738	PM	1	1
18	RNA1	PM	Allo738	1	1
19	RNA1	Allo738	PM	2	2
20	RNA1	PM	Allo738	2	2
21	RNA2	Allo738	PM	1	3
22	RNA2	PM	Allo738	1	3
23	RNA2	Allo738	PM	2	4
24	RNA2	PM	Allo738	2	4

table s2d. Microarray analysis of gene expression in flowers between Allo733 and parental mix.

Slide No.	Flower bud RNA	Cy3	Cy5	Printing Pattern	Dye-swap
25	RNA1	Allo733	PM	1	1
26	RNA1	PM	Allo733	1	1
27	RNA1	Allo733	PM	2	2
28	RNA1	PM	Allo733	2	2
29	RNA2	Allo733	PM	1	3
30	RNA2	PM	Allo733	1	3
31	RNA2	Allo733	PM	2	4
32	RNA2	PM	Allo733	2	4

table S2e. Microarray analysis of gene expression in flowers between Allo738 and parental mix.

Slide No.	Flower bud RNA	Cy3	Cy5	Printing Pattern	Dye-swap
33	RNA1	Allo738	PM	1	1
34	RNA1	PM	Allo738	1	1
35	RNA1	Allo738	PM	2	2
36	RNA1	PM	Allo738	2	2
37	RNA2	Allo738	PM	1	3
38	RNA2	PM	Allo738	1	3
39	RNA2	Allo738	PM	2	4
40	RNA2	PM	Allo738	2	4

table S2f. Microarray analysis of gene expression in leaves between A. thaliana diploid (At2) and autotetraploid (At4).

Slide No.	Flower bud RNA	Cy3	Cy5	Printing Pattern	Dye-swap
41	RNA1	At2	At4	1	1
42	RNA1	At4	At2	1	1
43	RNA1	At2	At4	2	2
44	RNA1	At4	At2	2	2
45	RNA2	At2	At4	1	3
46	RNA2	At4	At2	1	3
47	RNA2	At2	At4	2	4
48	RNA2	At4	At2	2	4

table S3. RT-PCR analysis of candidate genes detected by microarray analysis.

Locus	TAIR description	Symbol	RNA (UW)	RNA (TAMU)	Ratio (At4/Aa)	Ratio (Allo733/Mix)	Ratio (Allo738/Mix)	RT-PCR fragment (bp)	Primer sequences
AT5G56030	heat shock protein 81-2 (HSP81-2)	HSP90	+	+	0.90406	-0.6977	-0.87724	499	F: 5'-TGTCTCTGCAACCAAGGAAGGTC-3’ R: 5'-ATCGGCTTCAACAACATCATCGT-3’
AT5G12020	heat shock protein 17.6-II	HSP17.6b	+	-	1.4619	-1.02	-1.8317	494	F: 5'-CCGAAGACCACAACAACGAGAAG-3’ R: 5'-CCTCACGCATTCCGATTACATTC-3’
AT1G80840	WRKY family transcription factor	WRKY40	+	+	1.9652	-2.5912	-2.4936	465	F: 5’-GAAGATCCACCGACAAGTGCTTT-3’ R: 5’-TTTGACAGAACAGCTTGGAGCAC-3’
AT1G19610	plant defensin protein, putative (PDF1.4)	PDF1.4	+	+	1.0466	-0.60814	-0.57314	360	F: 5’-CCTTTGCCTCTCCATCTTCCTTA-3’ R: 5’-TCAAAGAAAATTCCCAAAAACCAA-3’
AT1G75830	plant defensin protein, putative (PDF1.1)	PDF1.1	+	+	-2.1055	0.83476	0.90425	322	F: 5’-CGCTGCTCTTGTTTTCTTTGCT-3’ R: 5’-AAACAAAGCAACATAACATATCTGG-3’
AT2G43590	glycosyl hydrolase family 19 (Chitinase)	CHI	+	+	n.s.	0.7796	0.89841	471	F: 5’-CGTAACTACTGCCAGAGCAGCAA-3’ R: 5’-GAACACCGAGACCCGACATAAAG-3’
AT3G15210	ethylene responsive element binding factor 4 (AtERF4)	ATERF4	+	+	0.97404	-1.021	-1.079	433	F: 5’-GACCCACAATAATGCCAAGGA-3’ R: 5’-TACGTTACCGATCCCCATCAG-3’
AT5G20230	blue copper binding protein	BCB	+	-	2.7399	-3.1919	-2.2944	599	F: 5’-GAAAAGGGGGTGACCTGAGTTCT-3’ R: 5’-AGCGACCAGAAAAGTAGCACCAC-3’
AT5G54190	NADPH:protochlorophyllide oxidoreductase	PORA	-	-	-0.9472	1.7914	0.78946	455	F: 5’-AAACCATTTGGGCCACTTTCTT-3’ R: 5’-CAAGTCTTTTCCCAGCCTCTGA
AT4G27440	protochlorophyllide reductase precursor	PORB	+	+	-1.2321	2.0486	2.189	433	F: 5’-ACCAAATCAAATCCGAACATGG-3’ R: 5’-GGCTCTTTAGCTGTCGGGAAAT-3’
AT3G46970	starch phosphorylase, putative	SPP	+	+	n.s.	1.0583	1.5007	499	F: 5’-GAAATTTGGGAGATAAGCGATGG-3’ R: 5’-ATAACCCCAAGCAGGCAGATTTA-3’
At3G02380	CONSTANS-like 2 (COL2)	COL2	+	+	0.77842	-0.71412	-0.73129	436	F: 5’-ACCACCTGTGATGCTCGAGTT-3’ R: 5’-CTCCTCCAAAGCTCCTCTGGT-3’
AT5G10140	MADS box protein FLOWERING LOCUS F (FLF)	FLC	+	+	-0.6118	0.78811	0.55986	617	F: 5’-AAATTAGGGCACAAAGCCCTCTC-3’ R: 5’-GTAGTGGGAGAGTCACCGGAAGA-3’
AT5G09810	Actin 2	Act2	+	+	n.s.	n.s.	n.s.	656	F: 5'-CTCATGAAGATTCTCACTGAG-3’ R: 5'-ACAACAGATAGTTCAATTCCCA-3’

Note: “+” matched microarray data; “-” did not match microarray data; “n.s.”: not significant; P-values associated with each gene are omitted in this table but displayed in table S1; Ratios shown are logarithm-fold changes in microarray analysis