Ontology highlight
ABSTRACT:
PROVIDER: PRJNA604488 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11006467_1.fastq.gz | Fastqsanger.gz | |||
| SRR11006467_2.fastq.gz | Fastqsanger.gz | |||
| SRR11006468_1.fastq.gz | Fastqsanger.gz | |||
| SRR11006468_2.fastq.gz | Fastqsanger.gz | |||
| SRR11006469_1.fastq.gz | Fastqsanger.gz |
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Project description:Methods: Panax notoginseng was used to treat MCAO model rats, and the differentially expressed genes between Panax notoginseng group and model group were identified by RNA SEQ, and the possible mechanism of Panax notoginseng in regulating ischemic stroke was analyzed
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Project description:Nitrogen is one of the essential elements for plant growth. NH4+ and NO3- are two major forms of absorbing element N for higher plants. In this study we found that the growth of Panax notoginseng is inhibited when only adding ammonium nitrogen fertilizer, and adding nitrate fertilizer can alleviate the toxicity caused by ammonium. We use RNA-seq to identify genes that are related to the alleviated phenotypes after introducing NO3- to Panax notoginseng roots under NH4+ stresses. Twelve RNA-seq profiles in four sample groups, i.e., control, samples treated with NH4+, samples treated with NO3- only, and treated with both NH4+ and NO3- were obtained and analyzed to identify deregulated genes in samples with different treatments. ACLA-3 gene is downregulated in NH4+ treated samples, but is upregulated in samples treated with NO3- and with both NH4+ and NO3-, which is further validated in another set of samples using qRT-PCR. Our results suggest that unbalanced metabolism of nitrogen and nitrogen is the main cause of ammonium poisoning in roots of Panax notoginseng, and NO3- may significantly upregulate the activity of ACLA-3 which subsequently enhances the citrate cycle and many other metabolic pathways in Panax notoginseng root. These potentially increase the integrity of the Panax notoginseng roots. Our results suggest that introducing NO3- fertilizer is an effective means to prevent the occurrence of toxic ammonium in Panax notoginseng root.
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Project description:The total RNA were extracted from tissues of roots from several plants of Panax notoginseng under CK and Cd stress treatment by using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. The purified PCR product was sequenced using Illumina Genome Analyzer II. The qualified reads were used to study of Panax notoginseng transcriptome under CK and Cd stress treatment.
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Project description:In current study, we observed that Panax notoginseng exosome-like nanoparticles successfully inhibited apoptosis and promoted proliferation in HSF. Moreover, transcriptomics was implemented to uncover its underlying mechanism. A total of 7924 differentially expressed genes (DEGs) were identified, with some of them enriched in apoptosis, proliferation related pathways. Intriguingly, some DEGs were annotated in skin aging development or coagulation function pathways. In view of this, we suggested Panax notoginseng exosomes may delay skin aging. Lastly, RT-qPCR confirmed the veracity and reliability of RNA-sequencing results.
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Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
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