Study : Transcriptome-wide analysis of gene expression using detached first-pair rosette leaves before culture (time 0) and 1 day after culture (DAC) from 9-day-old, 12-day-old and 15-day-old Col-0 seedlings

Identification

Name

Transcriptome-wide analysis of gene expression using detached first-pair rosette leaves before culture (time 0) and 1 day after culture (DAC) from 9-day-old, 12-day-old and 15-day-old Col-0 seedlings

Identifier

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Source

Data link

Link to this study on EBI European Nucleotide Archive

Description

To analyze the molecular mechanism behind the relationship between Arabidopsis leaf maturation and de novo root regeneration, we carried out an RNA-seq analysis using detached first-pair rosette leaves before culturing (time 0) and 1 d after culturing (DAC) from 9-, 12- and 15-d-old Col-0 seedlings. We first analyzed gene expression levels in the leaves before detachment (at time 0) from the three developmental states. Changes in gene expression could be grouped into six clusters. Many genes were upregulated or downregulated during leaf maturation. Next, we analyzed gene expression levels in the leaf explants from 9- and 15-d-old seedlings at 1 DAC compared with gene expression levels at time 0. By comparing up- or downregulated genes (1 DAC vs time 0) between leaves from 9- and 15-d-old seedlings, we found that many of the genes were particularly up- or downregulated only in immature leaves or only in mature leaves after 1 d of culturing. Overall design: RNA-Seq data for 9-, 12- and 15-d-old Col-0 seedlings grown under 24-h constant light conditions. Detached leaf explants were cultured on B5 medium without sucrose at 22°C under 24-h light conditions. Biological duplicates were performed for each developmental stage and treatment analyzed.

Data files

Genotype

Accession number	Name	Taxon