Lux.20000.R
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1214000 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Purpose: The goals of this study are to compare RNA-seq profiles of Col-0, acd6-1, Iux-1, and acd6-1lux-1 to identify genes affected by LUX. Methods: Total RNA was extracted from 25-d old Col-0, lux-1, acd6-1, or acd6-1lux-1 plants collected at ZT1 or ZT13. Triplicate biological samples were used for most genotypes at each time point, except acd6-1 and acd6-1lux-1 at ZT13, which had duplicate samples. 0.5 ug RNA per replicate was used to generate cDNA libraries using Illumina TruSeq RNA sample preparation kit (catalog no. RS-122-2001). The samples were multiplexed and sequenced using the Illumina HiSeq sequencing platform in Genomics Resources Core Facility at Weill Cornell Medical College. Sequencing was conducted with a standard run of 51 cycles and single reads. At least 150 million reads per lane were obtained for sequencing. qRT–PCR validation was performed using TaqMan and SYBR Green assays for some selected genes. Results: We found that over 1500 genes are affected by lux-1 based on the RNAseq analysis. GO analysis revealed that LUX-affected genes are enchriched in response to abiotic and biotic stimuli. In particular, genes involved in basal defense, salicyclic acid signaling, and jasmonic acid signaling are affected by lux-1. We also found LUX regulation of the clock genes, including core clock components and those acting in the output pathways. Conclusions: The RNAseq analysis support a role of LUX in regulation of the circadian clock and plant defense.
2019-06-12 | GSE115680 | GEO
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 |
Project description:Plants trigger leaf senescence to relocate energy and nutrients from aging leaves to developing tissues or storage organs to optimize the growth and reproduction under limited nutrients and energy conditions. Jasmonate signaling is one of the major endogenous hormone signals to induced leaf senescence in Arabidopsis. However, whether circadian clock will gate Jasmonate signaling to induce leaf senescence and the underlying precise mechanism is unclear. Here we find that the Evening Complex (EC) of core oscillator closely regulates leaf senescence. To identify the underlying mechanism of EC regulating leaf senescence, we conducted RNA-sequencing. Transcriptomic data reveals Evening complex extensively involves into JA signal transduction and responses. Moreover, the mutants of ELF3, ELF4 and LUX universly display the accelerated JA-induced leaf senescence phenotype, while their overexpression lines act reversely. In accordance with the transcript levels of JA immediate early induced JA-responsive gene MYC2 are up-regulated in lux mutants. Futhermore we demonstrated LUX can bind to to the promoter of MYC2 in vivo to represses its transcription. In addition, the accelerated JA-induced leaf senescence in mutants of evening complex can be overturned by myc2, myc3 and myc4 mutants redundantly. Collectively, our findings demonstrated the underlying molecular basis for circadian clock gating jasmonate signaling to induce leaf senescence through the module of evening complex to directly repressing MYC2 transcription. This novel established molecular module also refines complicated nodes between circadian clock and jasmonate signal in Arabidopsis.
2018-02-06 | GSE99290 | GEO
Project description:Next Generation Sequencing to Study LUX-affected genes.
| PRJNA475754 | ENA
Project description:Arabidopsis thaliana circadian and light signaling mutants have long hypocotyls under light/dark cycles. In order to determine if aberrant hypocotyl growth is due to time of day specific miss-expression of growth associated transcripts we conducted time course microarray experiments in the lux-2, lhy and phyB-9 mutants. The mutants and their parental genotypes were grown on plates under either intermediate days (12 hours light and 12 hours dark) for lux-2, or short day (8 hrs of light and 16 hrs of dark) for lhy and phyB-9, for seven days and tissue was collected every four hours over one day.
2008-10-17 | E-MEXP-1299 | biostudies-arrayexpress
Project description:Purpose: The goal of this study is to compare endothelial small RNA transcriptome to identify the target of OASL under basal or stimulated conditions by utilizing miRNA-seq. Methods: Endothelial miRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads. rRNA removed reads are sequentially aligned to reference genome (GRCh38) and miRNA prediction is performed by miRDeep2. Results: We identified known miRNA in species (miRDeep2) in the HUVECs transfected with siCTL or siOASL. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of endothelial miRNA profiles affected by OASL knockdown with biologic replicates.
2022-09-06 | GSE186354 | GEO
Project description:A cDNA library was constructed by Novogene (CA, USA) using a Small RNA Sample Pre Kit, and Illumina sequencing was conducted according to company workflow, using 20 million reads. Raw data were filtered for quality as determined by reads with a quality score > 5, reads containing N < 10%, no 5' primer contaminants, and reads with a 3' primer and insert tag. The 3' primer sequence was trimmed and reads with a poly A/T/G/C were removed
2021-07-21 | GSE180131 | GEO