Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA317861 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Long intergenic noncoding RNAs (lincRNAs), Natural Antisense Transcripts (NATs), and microRNAs (miRNAs) play important roles in many biological processes. To profile circadian regulated long noncoding RNAs (lncRNAs), we grow Arabidopsis plants (Col-0) under short day SD (8h light/16h dark) condition and used the ATH lincRNA v1 array to profile lincRNA, NAT and miRNA gene expression under continuous light condition. Using JTK_CYCLE to search for cycling expression pattern of genes, we found ~900 genes encoding lincRNAs, NATs and miRNAs showed significant cycling expression patterns (Adjusted P-value < 0.05).
2017-08-11 | GSE80094 | GEO
Project description:Purpose: Circadian clock in plants temporally coordinates biological processes throughout the day synchronizing gene expression with environmental changes. Here, we examined the genome-wide circadian and diurnal control of Arabidopsis transcriptome using high throughout RNA-seq approach. Methods: Transcriptional and posttranscritional profiles were identified and characterized for Arabidopsis seedlings grown under continuous light or long-day condition (16 h light/8 h dark) for one day (each condition has two biological replicates). Results: We show that rhythmic posttranscriptional regulation is also a significant factor for genome-wide profile of circadian plant transcriptome. Two major posttranscriptioal mechanisms alternative splicing (AS) and alternative polyadenylation (APA) show circadian rhythmicity, resulting from the oscillation in the genes invovled in AS and APA. Conclusions: Arabidopsis circadian clock not only controls the transcription of genes, but also affects their posttranscriptional regulation through regulating AS and APA.
2020-01-14 | GSE137732 | GEO
Project description:Arabidopsis AP1-GR ap1-1 cal-1 were grown under long-day (16 h light/8 h dark) condition. After bolding (26 DAG), half of the plants were treated with dexamethasone. 31 DAG, the untreated inflorescenes were sampled as t0 and the dexamethasone treated one as t5.
2022-10-23 | GSE159988 | GEO
Project description:We systematically identified long noncoding natural antisense transcripts (lncNATs), defined as lncRNAs transcribed from the opposite DNA strand of coding or noncoding genes. We identified in total 37,238 sense-antisense transcript pairs and found 70% mRNAs are associated with antisense transcripts in Arabidopsis. To investigate the role of NATs in response to white light treatment, we designed an Agilent custom array, ATH NAT array, and analyzed WT seedlings grown in the dark (0h) and seedlings undergoing de-etiolation in continuous white light for 1h and 6h. To obtain information on organ-specific transcriptome profiles, we further dissected seedlings into cotyledons, hypocotyls and roots. We examined the abundance of NATs in etiolated seedlings and seedlings undergoing de-etiolation in continuous white light for 1/6h. Seedlings were further dissected into cotyledons, hypocotyls and roots. RNAs from 3 biological replicates of each of the 3 organs were separately hybridized to ATH NAT arrays to profile light-regulated NAT pairs.
2013-12-23 | E-GEOD-49382 | biostudies-arrayexpress
Project description:We sequenced the poly(A)+ and poly(A)- samples of the roots and shoots from 10-day-old WT seedlings grown under P+ and P- condition. The WT plant refers to Columbia ecotype Arabidopsis seedlings. Each condition has two replicates. After total RNA extraction, ribosomal RNAs were removed using RiboMinus™ Plant Kit repeated two times. The poly(A)+ and poly(A)- constituent were separated with oligo(dT) magnetic beads (Oligotex mRNA Mini Kit, QIAGEN). Using a 2-fold change and a P-value <0.05 as the cut-off for selecting the differentially expressed transcripts, we globally identified novel noncoding lncRNAs.
2016-08-31 | GSE76577 | GEO
Project description:Arabidopsis thaliana transcriptome over light-dark and continuous light time-course.
| PRJNA843855 | ENA
Project description:Arabidopsis grafted long-noncoding RNA sequencing data
| PRJNA1288436 | ENA
Project description:We systematically identified long noncoding natural antisense transcripts (lncNATs), defined as lncRNAs transcribed from the opposite DNA strand of coding or noncoding genes. We identified in total 37,238 sense-antisense transcript pairs and found 70% mRNAs are associated with antisense transcripts in Arabidopsis. To investigate the role of NATs in response to white light treatment, we designed an Agilent custom array, ATH NAT array, and analyzed WT seedlings grown in the dark (0h) and seedlings undergoing de-etiolation in continuous white light for 1h and 6h. To obtain information on organ-specific transcriptome profiles, we further dissected seedlings into cotyledons, hypocotyls and roots.
2013-12-23 | GSE49382 | GEO
Project description:Reticulon family proteins are membrane-spanning proteins localized in the endoplasmic reticulum (ER) and are present in all eukaryotes. In animal cells, these proteins, known as reticulons, have a wide range of functions. These functions encompass involvement in vesicle formation, ER membrane morphogenesis, and the inhibition of nerve regeneration. Conversely, in plants, our understanding of the function of reticulon-like family proteins (RTNLBs) remains limited. In the plant Arabidopsis, the RTBLB gene family comprises twenty-one members, with RTNLB16 being the most intricate. The AtRTNLB16 gene consists of seven splice variants, each encoding seven distinct protein isoforms. An Arabidopsis T-DNA mutant (Salk_122275/rtnlb16-1), which is a knockout for the upper coding frame isoform 7 while concurrently overexpressing the other isoforms through the CaMV 35S promoter at the left border of the T-DNA insertion, exhibits growth retardation, reduced chlorophyll levels, and insensitivity to abscisic acid or senescence stimuli. Under a diurnal regime of 16 hours of light followed by 8 hours of darkness, which activates the 35S promoter, the expression of RTNLB16 transcripts in the rtnlb16-1 mutant intensifies, resulting in profound growth inhibition. Conversely, growing under a continuous low-light (CLL) condition curbs the overexpression and mitigates this phenotype. Under a diurnal regime of 16 hours of light followed by 8 hours of darkness, which activates the 35S promoter, the expression of RTNLB16 transcripts in the rtnlb16-1 mutant intensifies, resulting in profound growth inhibition. Conversely, growing under a continuous low-light (CLL) condition curbs the overexpression and mitigates this phenotype. We utilized the altered expression of the RTLB16 gene in this mutant line due to its dependence on the light regime. Our aim was to uncover the biological processes in which it participates. To achieve this, we conducted RNA sequencing on leaves from four-week-old wild-type (Col-0) and rtnlb16-1 plants grown under CLL or 16:8 light regimes.
2026-07-22 | GSE242257 | GEO
Project description:Long Intergenic Noncoding RNAs regulated by SERRATE, CBP20 and CBP80
| PRJNA152059 | ENA