Table I. Analysis of DEGs of nonacclimated reil1-1 reil2-1 relative to the nonacclimated Col-0 wild type (0 d) that also were cold-responsive transcripts of the Col-0 wild type at 1 day, 1 week, or 3 weeks after the shift to 10°C relative to nonacclimated Col-0.

Nonacclimated reil1-1 reil2-1 and Col-0 (0 d) were compared by heteroscedastic Student’s t testing at P < 0.01 (n = 5–6 independent pools of mature rosette leaves from two to three plants). 10°C cold-responsive transcripts were selected at P < 0.01 (n = 3 independent pools of mature rosette leaves from two to three plants). The set of 428 DEGs and the subset of 150 genes that also were 10°C shift responsive in Col-0 are reported in Supplemental Table S3. The column 1 d, 1 w, or 3 w lists the sum of genes that were differentially expressed during at least one time point; the column 1 d, 1 w, and 3 w lists the number of genes that were differentially expressed at all time points.

Plant and Parameter	0 d	1 d	1 Week	3 Weeks	1 d, 1 w, or 3 w	1 d, 1 w, and 3 w
Col-0
All	–	3,301	2,711	3,275	6,537	594
Up	–	2,726	2,323	2,682	5,310	538
Down	–	575	388	593	1,227	56
		Number of DEGs that also were 10°C shift responsive in Col-0
reil1-1 reil2-1
Count
All	428	80	77	100	150	31
Up	287	66	67	86	121	31
Down	141	14	10	14	29	0
Percentage relative to day 0
All	100.0	18.7	18.0	23.4	35.0	7.2
Up	100.0	23.0	23.3	30.0	42.2	10.8
Down	100.0	9.9	7.1	9.9	20.6	0.0