Ontology highlight
ABSTRACT:
PROVIDER: PRJNA753939 | ENA |
REPOSITORIES: ENA
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Project description:C3-C4 intermediate Moricandia suffruticosa showed tolerance to drought and heat stresses, and high photosynthetic capacity under these abiotic stresses as comparing with C3 relative crop rapeseed (Brassica napus). In our study, systematic analysis was conducted to reveal photosynthetic difference between C3-C4 Moricandia suffruticosa and its relative C3 rapeseed from the same Brassiceae tribe. It was found that Moricandia leaf photosynthesis and anatomy were significantly changed compared to rapeseed under drought and heat stress conditions. De novo transcriptome of Moricandia was assembled by next generation sequencing, and unigenes were mapped to respective rapeseed gene locus. Then comparative transcriptome analysis was conducted in leaf tissues of Moricandia and rapeseed under both drought and heat stresses. Main pathways and candidate genes were revealed from this analysis, which may be associated with the stress induced change in Moricandia.
2020-08-12 | GSE156029 | GEO
Project description:We performed ATAC-sequencing in LSK cells (Lin(neg)/c-Kit(+)/Sca-1(+)) from shRNA mice carrying an shRNA for either Renilla or Stag2. ATAC-sequencing control (Renilla) and Stag2 knockdown cells.
2015-09-16 | E-GEOD-72367 | biostudies-arrayexpress
Project description:We describe an assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, as a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol with 500–50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. We discovered classes of DNA-binding factors that strictly avoided, could tolerate or tended to overlap with the nucleosome. Using ATAC-seq maps of human CD4+ T cells from a proband obtained on consecutive days, we demonstrated the feasibility of analyzing an individual’s epigenome on a timescale compatible with clinical decision-making. We examined chromatin structure using ATAC-seq in 2 cell types (GM12878 cell line, purified CD4+ T cells).
2013-10-01 | E-GEOD-47753 | biostudies-arrayexpress
Project description:Oil rapeseed (Brassica napus L.) is a typical winter biennial plant, with high cold tolerance during vegetative stage. In recent years, more and more early-maturing rapeseed varieties were planted across China. Unfortunately, the early-maturing rapeseed varieties with low cold tolerance have higher risk of freeze injury in cold winter and spring. Little is known about the molecular mechanisms for coping with different low-temperature stress conditions in rapeseed. In this study, we investigated 47,328 differentially expressed genes (DEGs) of two early-maturing rapeseed varieties with different cold tolerance treated with cold shock at chilling (4°C) and freezing (−4°C) temperatures, as well as chilling and freezing stress following cold acclimation or control conditions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that two conserved (the primary metabolism and plant hormone signal transduction) and two novel (plant-pathogen interaction pathway and circadian rhythms pathway) signaling pathways were significantly enriched with differentially-expressed transcripts. Our results provided a foundation for understanding the low-temperature stress response mechanisms of rapeseed. We also propose new ideas and candidate genes for genetic improvement of rapeseed tolerance to cold stresses.
2020-03-19 | GSE129220 | GEO
Project description:MicroRNAs (miRNAs) are a class of non-coding small RNAs (sRNAs) that play crucial regulatory roles in various developmental processes. Silique length indirectly influences seed yield in rapeseed (Brassica napus); however, the molecular roles of miRNAs in silique length are largely unknown. Here, backcross progenies of rapeseed with long siliques (LS) and short siliques (SS) were used to elucidate this role. Four small RNA libraries from early developing siliques were sequenced, and a total of 814 non-redundant miRNA precursors were identified, representing 65 known miRNAs, and 394 novel miRNAs. Expression analyses revealed 12 known miRNAs and 5 novel miRNAs that were differentially expressed in LS and SS lines. Furthermore, though two degradome sequencing, we annotated 522 cleavage events. An analysis of correlated expression between differentially expressed miRNAs and their targets demonstrated that some transcription factors might repress cell proliferation or auxin signal transduction to control silique length, and that a Pi/Cu deficiency might also restrict silique development. More significantly, the overexpression of miR160 in rapeseed may repress auxin response factors and result in increased silique length, illustrating that silique length could be regulated via an auxin-response pathway. These results will serve as a foundation for future research in B. napus.
2019-08-01 | GSE107056 | GEO
Project description:This experiment includes the sequencing files for different hp1a-tn5 hybrids, together with standard ATAC-seq and ChIP-seq data used to evaluate the best construct.
2021-08-17 | E-MTAB-9648 | biostudies-arrayexpress
Project description:Compared to ordinary rapeseed, high-oleic acid rapeseed has higher levels of monounsaturated fatty acids and lower levels of saturated fatty acid and polyunsaturated fatty acids, and thus is of high nutritional and health value. In addition, high-oleic acid rapeseed oil imparts cardiovascular protective effects. Based on these properties, high-oleic acid oil crops have been extensively investigated and cultivated. In this study, we employed a microarray analysis with high oleic acid line and low oleic acid line from the developing seeds (27 days after flowering) of Brassica napus.
2018-09-20 | GSE120223 | GEO
Project description:This study investigates the transcriptome and physiological responses of rapeseed to post-flowering temperature increases, providing valuable insights into the molecular mechanisms underlying rapeseed tolerance to heat stress. Two rapeseed genotypes, Lumen and Solar, were assessed under control and heat stress conditions in field experiments conducted in Valdivia, Chile. Results showed that seed yield and seed number were negatively affected by heat stress, with genotype-specific responses. Lumen exhibited a 9.3% average seed yield reduction, while Solar showed a 28.7% reduction. RNA-seq analysis of siliques and seeds revealed tissue-specific responses to heat stress, with siliques being more sensitive to temperature stress. Hierarchical clustering analysis identified distinct gene clusters reflecting different aspects of heat stress adaptation in siliques, with a role for protein folding in maintaining silique development and seed quality under high temperature conditions. In seeds, three distinct patterns of heat-responsive gene expression were observed, with genes involved in protein folding and response to heat showing genotype-specific expression. Gene coexpression network analysis revealed major modules for rapeseed yield and quality, as well as the trade-off between seed number and seed weight. Overall, this study contributes to understanding the molecular mechanisms underlying rapeseed tolerance to heat stress and can inform crop improvement strategies targeting yield optimization under changing environmental conditions.
2023-09-02 | GSE241954 | GEO