https://doi.org/10.5061/dryad.5mkkwh7ch

Description of the data and file structure

This data includes the following sheets.

Field data

Seasonal time-series transcriptome and genome-wide H3K4me3 and H3K27me3 data from Arabidopsis halleri (Nishio et al., 2020b).

Transcript and ChIP-seq data are shown as log2 (RPKM+1).

• Ahal_ID: Gene ID in A. halleri .
• Araport11_ID: Homologues gene ID in A. thaliana.
• Reciprocal_flag: Number of homologues gene in A. halleri for the homologues genes in A. thaliana.
• Locus_type: Whether the locus encodes a protein.
• Symbol: Gene name.
• Alias: The other gene name.
• Note: Short description.
• Transcript: Gene expression (mRNA) levels in each month.
• ChIP-seq/H3K4me3/Gene body: H3K4me3 levels within a 1 kilobase (kb) region downstream of the TSS (Transcription start site).
• ChIP-seq/H3K27me3/Gene body: H3K27me3 levels within a 1 kb region downstream of the TSS.
• ChIP-seq/H3K4me3/Promoter: H3K4me3 levels within a 2 kb region upstream of the TSS.
• ChIP-seq/H3K27me3/Promoter: H3K27me3 levels within a 2 kb region upstream of the TSS.
• _max: Maximum level of 12 months data in each category.
• _min: Minimum level of 12 months data in each category.
• Correlation coefficient: Spearman’s rank correlation coefficients (ρ).

Fig1, FigS1, FigS2, FigS3

Promoter-gene overlap

Length of overlap (bp) between the promoter region (2kb upstream) and other genes for  all genes from A.halleri.

FigS1

RT-qPCR

Relative expression levels of genes in the cold treatment experiments. Values were normalized to the internal control and to the average values before temperature treatment (0d = 1).

The descriptions of "Time point"  are as follows.

0d: After pre-treatment growth, and before temperature treatment.

dC: Number of days in cold condition after pre-treatment growth.

dW: Number of days in warm condition after pre-treatment growth.

Fig2, Fig4, Fig5, FigS5, FigS7

RT-qPCR (Warm break) 

Relative expression levels of genes in the warm break experiments. Values were normalized to the internal control and the to average values before temperature treatment (0d = 1).

The descriptions of "Time point"  are as follows.

0d: After pre-treatment growth, and before temperature treatment.

dC: Number of days in cold condition.

dW: Number of days in warm condition.

e.g.) 1dC-3dW-1dC: After pre-treatment growth, 1 day cold and 3 days warm and 1 day cold treatment.

FigS8

ChIP-qPCR

Accumulation levels of H3K27me3 and H3K4me3 in the cold treatment experiments. Values were normalized to the internal control loci and to the H3 levels.

The descriptions of "Time point"  are as follows.

0d: After pre-treatment growth, and before temperature treatment.

dC: Number of days in cold condition after pre-treatment growth.

dW: Number of days in warm condition after pre-treatment growth.

Fig2, Fig4

t-test (qPCR)

P-values in t-test for qPCR data. 

t-test for ChIP-qPCR, RT-qPCR: Welch, two-sided

t-test for RT-qPCR (Warm break): Welch, two-sided, adjusted by Sequential Bonferroni correction for multiple comparison

GUS

The number of pixels in unstained (no_non) and GUS-stained (no_gus) areas for quantification of the GUS signals.

no_gus/no_non shows the ratio of GUS-stained (no_gus) to unstained tissue areas (no_non).

Fig3

Flowering time

Number of leaves at time of flowering.

0d, 7dC and 14dC show the temperature treatment conditions of the plants used in the flowering time measurement experiment.

The descriptions of the temperature treatment conditions are as follows.

0d: After pre-treatment growth, and before temperature treatment.

dC: Number of days in cold condition after pre-treatment growth.

Fig5

Petiole length

Petiole lengths (mm) after the temperature treatments.

The descriptions of the temperature treatment conditions are as follows.

0d: After pre-treatment growth, and before temperature treatment.

dC: Number of days in cold condition after pre-treatment growth.

Fig5

t-test (Fig5, FigS5)

P-values in t-test for the data in Fig5 and FigS5. 

t.test: Welch, two-sided, adjusted by sequential Bonferroni correction for multiple comparison