Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA125845 | ENA |
REPOSITORIES: ENA
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Project description:The hypocotyl of Arabidopsis seedlings shows rhythmic periods of elongation. The patterns of elongation are controlled by a combination of internal factors, such as the circadian clock, and external factors such as light. In a previous study we had found that two transcription factors, PIF4 and PIF5 are important integrators of clock and light signals for the control of elongation. Here we use microarrays to find genes that are correlated with elongation and that are controlled by PIF4 and/or PIF5. Arabidopsis seedlings grown under short day conditions for three days were transferred to SD/3 conditions (160 min light: 320 min dark cycles) from the dawn of the fourth day. Seedlings were then collected during periods of hypocotyl elongation and stasis for three days. There are two types of replication: temporal and independent experiments. For temporal replication, samples collected at the same time of day on subsequent days were used as replicates. In addition, replicate samples were collected in two independent time courses for most time points. Col and CCA1OX samples from the first time course for time points 280, 1240, 1720, 2680, 3160, and 4120 were originally deposited under GEO Series GSE6906; they have been re-analyzed for this study. Each sample consists of multiple pooled seedlings.
2011-03-31 | E-GEOD-21684 | biostudies-arrayexpress
Project description:Plants have the capacity to sense and respond to even small changes in ambient temperature. Numerous thermomorphogenic responses can be observed in Seedlings including elongation of the hypocotyl, petioles and the primary root while leaf blade areas are reduced. Main objective of the experiment was the assessment of tissue-specific transcriptome responses in Arabidopsis seedlings exposed to elevated ambient temperatures, 5 days old Arabidopsis seedlings grown at 20°C in LD were shifted for 3 or 24h to 28°C. Control plants were kept at 20°C. At time of harvest, cotyledons and roots were dissected and collected separately from the hypocotyl. To minimize circadian effects, plant material was grown in several successive batches and harvested only for a period of 30 min per timepoint on several consecutive days. Shifts and harvest was performed at midday to late afternoon (see ZT in overall design).
2019-02-12 | GSE126373 | GEO
Project description:Plants have evolved shoot elongation mechanisms to escape from diverse environmental stresses such as flooding and vegetative shade. The apparent similarity in growth responses suggests possible convergence of the signalling pathways. Shoot elongation is mediated by passive ethylene accumulating in flooded plant organs and by changes in light quality and quantity under vegetation shade. Here we study hypocotyl elongation as a proxy for shoot elongation and delineated Arabidopsis hypocotyl length kinetics in response to ethylene and shade. Based on these kinetics, we further investigated ethylene and shade-induced genome-wide gene expression changes in hypocotyls and cotyledons separately. Both treatments induced a more extensive transcriptome reconfiguration in the hypocotyls compared to the cotyledons. Bioinformatics analyses suggested contrasting regulation of growth promotion- and photosynthesis-related genes. These analyses also suggested an induction of auxin, brassinosteroid and gibberellin signatures and the involvement of several candidate regulators in the elongating hypocotyls. Pharmacological and mutant analyses confirmed the functional involvement of several of these candidate genes and physiological control points in regulating stress-escape responses to different environmental stimuli. We discuss how these signaling networks might be integrated and conclude that plants, when facing different stresses, utilise a conserved set of transcriptionally regulated genes to modulate and fine tune growth. 1 day old Arabidopsis seedlings were subjected to control, ethylene and shade conditions. Hypocotyl and cotyledon tissues were harvested at 1.5 h, 13.5 h and 25.5 h of treatment time respectively. Microarray hybridization was carried out with 3 biological replicates (collected over 3 independent experiments) of each sample using the Affymetrix Arabidopsis Gene 1.1 ST platform.
2016-06-10 | E-GEOD-83212 | biostudies-arrayexpress
Project description:Light- and Phytochrome-Dependent Regulation of Hypocotyl Elongation in Arabidopsis thaliana
| PRJNA170166 | ENA
Project description:The hypocotyl of Arabidopsis seedlings shows rhythmic periods of elongation. The patterns of elongation are controlled by a combination of internal factors, such as the circadian clock, and external factors such as light. In a previous study we had found that two transcription factors, PIF4 and PIF5 are important integrators of clock and light signals for the control of elongation. Here we use microarrays to find genes that are correlated with elongation and that are controlled by PIF4 and/or PIF5.
2011-03-31 | GSE21684 | GEO
Project description:We report POWERDRESS (PWR), a SANT domain containing protein known to facilitate the deacetylation of lysine rich residues of histone H3 by HISTONE DEACETYLASE 9 (HDA9), to play key role in temperature induced growth in Arabidopsis thaliana. Mutations in PWR showed severe attenuation in high temperature associated phenotypes viz., temperature-induced hypocotyl elongation, petiole elongation and early flowering. The study involved analysing the impact of the loss of PWR on the transcriptome in response to changes in ambient temperature. About one hundred 6 day old seedlings of wild type (Col-0) and pwr-2 mutant (in Col-0 background) were grown at 23 °C in short days (SD) photoperiod in growth chambers (GR-36, Percival Scientific, Canada). Half of the samples were then shifted to 27°C under short day photoperiod. Total RNA was extracted from whole seedlings grown at 23 °C and 27°C after two hours. Two biological replicates were used for Col-0 and pwr-2 samples. RNA was extracted using Isolate II RNA plant kit (Bioline Pty Ltd, Australia). RNA-Seq libraries were generated on Illumina HiSeqTM 2000 platform using paired-end sequencing of 90 bp in length at BGI-Shenzen (Beijing Genomics Institute). Gene expression analysis was performed using DESeq2 (v1.14.1) differential expression analysis pipeline.
2017-12-01 | GSE101782 | GEO
Project description:During de-etiolation of Arabidopsis seedlings, light promotes the expansion of cotyledons but inhibits the elongation of hypocotyls. The mechanism of this differential regulation of cell enlargement is unclear. Our organ-specific transcriptomic analysis identified 32 Small Auxin Up RNA (SAUR) genes whose transcripts were light-induced in cotyledons and/or repressed in hypocotyls. We therefore named these SAURs as lirSAURs. Both overexpression and mutation analyses demonstrated that lirSAURs could promote cotyledon expansion and opening and enhance hypocotyl elongation, possibly by inhibiting phosphatase activity of PP2C-Ds. Light reduced auxin levels to down-regulate the expression of lirSAURs in hypocotyls. Further, phytochrome-interacting factors (PIFs) were shown
2016-05-03 | GSE79576 | GEO
Project description:cotyledon and hypocotyl specific whole-genome transcriptome (mRNA-Seq) analysis of Arabidopsis seedlings exposed to low and high R:FR ratio
2017-07-15 | GSE59722 | GEO
Project description:Stimulation of cell elongation by tetraploidy in hypocotyls of dark-grown Arabidopsis seedlings
| PRJNA285262 | ENA
Project description:Transcriptional profiling of Arabidopsis wild-type (Col0) control seedlings with corresponding mutant seedlings is performed using Aligent's Whole Arabidopsis Gene Expression Microarray (G2519F, V4, 4x44K).
2017-02-09 | GSE39898 | GEO