Table 1 Summary of transcriptomes used for lncRNA annotation.

Transcriptome classification	Experiment	Age	Organ or tissue	Number of transcriptomes
Baseline	miRNA expression in embryos	3 days after pollination	Embryos	2
Baseline	Development stages of the apical meristem	7 to 16 days	SAM	30
Baseline	Search for lncRNAs	8 days	Seedlings	4
Baseline	Search for lncRNAs	14 to 35 days	Root, flower, fruit, and leaf	4
Baseline	Tissue Atlas	7 to 54 days	Multiple tissues	56
Baseline	Stages of silique development	0 to 20 days	Silique	4
Differential expression	Red light response	5 days	Hypocotyl and cotyledons	57
Differential expression	Response to blue light	3 days	Seedlings	6
Differential expression	Iron deficiency	13 days	Seedlings	6
Differential expression	Phosphate deficiency	13 days	Seedlings	6
Differential expression	Cold acclimatization	14 days	Seedlings	6
Differential expression	Response to prolonged cold	14 days	Seedlings	6
Differential expression	ABA treatment	14 days	Seedlings	17
Differential expression	Drought response	14 days	Seedlings	10

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