Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1136433 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29842275_1.fastq.gz | Fastqsanger.gz | |||
| SRR29842275_2.fastq.gz | Fastqsanger.gz | |||
| SRR29842276_1.fastq.gz | Fastqsanger.gz | |||
| SRR29842276_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:N6-methyladenosine (m6A) is a crucial epigenetic modification in mRNA and the most abundant methylation in eukaryotes. However, research on m6A modification in radish (Raphanus sativus) is not as extensive as in model plants. In this study, we analyzed m6A modification during the vegetative and reproductive growth stages of radish using m6A-seq and RNA-seq to explore its potential role in bolting and flowering. The results showed that m6A peaks significantly increased during the reproductive growth stage compared to the vegetative stage, with more m6A modification sites in the stop codon, 3' UTR, and promoter regions. Overexpression of the RsALKBH10B gene led to a global reduction in m6A modification and resulted in an early bolting and flowering phenotype, with transcription levels of key flowering factors RsSOC1 and RsFT increasing by 10-40 fold. Correlation analysis between differential m6A modification and differentially expressed genes indicated that genes such as RsSUF4, RsAGL13, and RsCDF5 might regulate bolting and flowering. Overexpression of RsSUF4 delayed bolting and flowering and decreased overall m6A modification levels; in positive transgenic plants, higher m6A levels of RsSUF4 were associated with lower transcription levels. These findings suggest that m6A methylation may regulate gene expression related to bolting and flowering in radish by affecting mRNA stability, ultimately leading to bolting and flowering.
2024-06-22 | GSE270351 | GEO
Project description:Bulked segregant analysis (BSA) is an efficient method to rapidly and efficiently map genes responsible for mutant phenotypes. This procedure, however, requires access to quantitative genetic markers that are polymorphic in the mapping population. We have developed a modification of BSA (BSR-Seq) that makes use of RNA-Seq reads to efficiently map genes even in populations for which no polymorphic markers have been previously identified. Because of the digital nature of next-generation sequencing (NGS) data, it is possible to conduct de novo SNP discovery and quantitatively genotype BSA samples using the same RNA-Seq data. In addition, analysis of the RNA-Seq data provides information on the effects of the mutant on global patterns of gene expression at no extra cost. In combination these results greatly simplify gene cloning experiments. To demonstrate the utility of this strategy BSR-Seq was used to clone the glossy3 (gl3) gene of maize. Mutants of the glossy loci exhibit altered accumulation of epicuticular waxes on juvenile leaves. We previously generated a large collection of glossy mutants using the Mu transposon system. By subjected a reference allele to BSR-Seq, we were able to map the gl3 locus to a ~2.3Mb interval that is consistent with the results of prior mapping experiments. The single gene located in the 2.3Mb mapping interval that contained a Mu insertion and whose expression was down-regulated in the mutant pool was subsequently demonstrated to be the gl3 gene via the analysis of multiple independently Mu transposon induced mutant alleles. The gl3 gene encodes a putative myb transcription factor, which directly or indirectly affects the expression of a number of genes involved in the biosynthesis of very-long-chain fatty acids.
2012-12-03 | E-MTAB-4234 | biostudies-arrayexpress
Project description:Bolting is a key process in the growth and development of lettuce (Lactuca sativa L.). High temperature can induce earlier bolting which decreases in both quality and production of lettuce. However, knowledge underlying lettuce bolting is still lacking. To better understand the molecular basis of bolting, a comparative proteomics analysis was conducted on lettuce stems in the bolting period induced by high temperature (33 °C) compared with a control (20 °C) using iTRAQ-based proteomics, phenotypic measures, and biological verifications. High temperature induced lettuce bolting, while control temperature did not. Of the 6656 proteins identified, 758 proteins significantly altered their expression level induced by high-temperature relative to the control, of which 409 were up-regulated and 349 down-regulated. Proteins with abundance level change were mainly involved in photosynthesis, carbohydrate metabolism, stress response, hormone synthesis, and signal transduction. These differential proteins were mainly enriched in pathways associated with photosynthesis and tryptophan metabolism involving in auxin (IAA) biosynthesis. Among the differentially expressed proteins associated with photosynthesis and tryptophan metabolism were up-regulated. Moreover, in gibberellin (GA) biosynthesis pathway, 10 of main enzymes of P450 were up-regulated. Proteins related to SAUR and GRP, implicated in IAA and GA signal transduction were up-regulated, and the phosphorylation and ubiquitination related proteins regulating IAA and GA signal transduction were also induced. These findings indicate that a high temperature enhances the function of photosynthesis, IAA and GA synthesis and signal transduction to promote the process of bolting, which is in line with the physiology and transcription levels of IAA and GA metabolism. Our data provide a first comprehensive dataset for gaining novel understanding of the molecular basis underlying lettuce bolting induced by high temperature. It is potentially important for further functional analysis and genetic manipulation for molecular breeding to breed new cultivar of lettuce to restrain early bolting, which is vital for improving vegetable quality.
2019-11-12 | PXD008610 | Pride
Project description:To investigate the mRNA m6A modification profiling in Mesocricetus auratus cells that infected with Senecavirus, we used passage-5 Senecavirus A to infect BSR-T7/5 cells. We then performed m6A MeRIP-seq(GenSeq®️ m6A MeRIP Kit) at at two time points (12hrs or 72 hrs after infection), each time point with three replicates.
2022-06-30 | GSE206974 | GEO
Project description:Lettuce (Lactuca sativa L.) is one of the most important leafy vegetable that is consumed during its vegetative growth. The transition from vegetative to reproductive growth is induced by high temperature, which has significant economic effect on lettuce production. However, the progression of floral transition and the molecular regulation of bolting are largely unknown. Here we morphologically characterized the inflorescence development and functionally analyzed the FLOWERING LOCUS T (LsFT) gene during bolting regulation in lettuce. We described the 8 developmental stages during floral transition process. The expression of LsFT was negatively correlated with bolting in different lettuce varieties, and was promoted by heat treatment. Overexpression of LsFT could recover the late-flowering phenotype of ft-2 mutant. Knockdown of LsFT by RNA interference dramatically delayed bolting in lettuce, and failed to respond to high temperature. Therefore, this study dissects the process of inflorescence development and characterizes the role of LsFT in bolting regulation in lettuce.
2018-02-14 | GSE108260 | GEO