Transcriptomics

Dataset Information

16

Transcription profiling of Arabidopsis seedlings grown under thermocycles and/or photocycles or continuous conditions


ABSTRACT: In most organisms biological processes are partitioned, or phased to specific times over the day through interactions between external cycles of temperature (thermocycles) and light (photocycles), and the endogenous circadian clock. This orchestration of biological activities is achieved in part through an underlying transcriptional network. To understand how thermocycles, photocycles and the circadian clock interact to control time of day specific transcript abundance in Arabidopsis thaliana, we conducted four diurnal and three circadian two-day time courses using Affymetrix GeneChips (ATH1). All time courses were carried out with seven-day-old seedlings grown on agar plates under thermocycles (HC, hot/cold) and/or photocycles (LD, light/dark), or continuous conditions (LL, continuous light; DD, continuous dark, HH, continuous hot). Whole seedlings (50-100), including roots, stems and leaves were collected every four hours and frozen in liquid nitrogen. The four time courses interrogating the interaction between thermocycles, photocycles and the circadian clock were carried out as two four-day time courses. Four-day time courses were divided into two days under diurnal conditions, and two days under circadian conditions of continuous light and temperature. Thermocycles of 12 hours at 22C (hot) and 12 hours at 12C (cold) were used in this study. The two time courses interrogating photoperiod were conducted under short days (8 hrs light and 16 hrs dark) or long days (16 hrs light and 8 hrs dark) under constant temperature. In addition, the photoperiod time courses were in the Landsberg erecta (ler) accession, in contrast to the other time courses that are in the Columbia (col) background. The final time course interrogated circadian rhythmicity in seedlings grown completely in the dark (etiolated). Dark grown seedlings were synchronized with thermocycles, and plants were sampled under the circadian conditions of continuous dark and temperature.

INSTRUMENT(S): 418 [Affymetrix]

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Todd P Michael  

PROVIDER: E-MEXP-1304 | ArrayExpress | 2008-01-18

REPOSITORIES: ArrayExpress

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Publications

Circadian oscillation of gibberellin signaling in Arabidopsis.

Arana María Verónica MV   Marín-de la Rosa Nora N   Maloof Julin N JN   Blázquez Miguel A MA   Alabadí David D  

Proceedings of the National Academy of Sciences of the United States of America 20110516 22


Circadian clocks are endogenous timekeeping mechanisms that allow organisms to anticipate rhythmic, daily environmental changes. Temporal coordination of transcription results in a set of gene expression patterns with peak levels occurring at precise times of the day. An intriguing question is how a single clock can generate different oscillatory rhythms, and it has been proposed that hormone signaling might act in plants as a relay mechanism to modulate the amplitude and the phase of output rhy  ...[more]

Publication: 1/2

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