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ABSTRACT: Three phytohormone-treated transcriptome of 1-year-old Panax notoginseng leaves

PROVIDER: PRJNA1129895 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29654526_1.fastq.gz	Fastqsanger.gz
	SRR29654526_2.fastq.gz	Fastqsanger.gz
	SRR29654527_1.fastq.gz	Fastqsanger.gz
	SRR29654527_2.fastq.gz	Fastqsanger.gz
	SRR29654528_1.fastq.gz	Fastqsanger.gz

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Nitrate fertilizer alleviates ammonium toxicity by enhancing ACLA-3 in Panax notoginseng roots

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.

2019-12-31 | GSE112437 | GEO

Effect of Panax Notoginseng on gene expression in rats with cerebral ischemia-reperfusion injury

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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RNA illumina sequencing of Panax notoginseng under CK and Cd stress treatment

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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MS data of tryptic peptides obtained through activity-guided protein purification

Project description:Protein band obtained from the Panax notoginseng leaves homogenate following an activity-guided protein-purification procedure, that showed regioselective ginsenoside hydrolysis activity was digested with trypsin and analyzed by Nano LC-LTQ Orbitrap MS to construct a peptide library of accessible amino acid sequences. Subsequent mutual sequence alignment analysis between the peptide and transcript libraries identified three candidate genes.

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Transcriptomics provides novel insights into the regulatory mechanism of Panax notoginseng exosome-like nanoparticles in HSF

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:Xuesaitong injection (XST), a standardized patent Chinese medicine of Panax notoginseng roots (Sanqi in Chinese), has long been used for effective prevention and treatment of stroke in China. However, the mechanisms underlying its effects against ischemic stroke are still poorly understood. In this study, we focused on the polypharmacology of XST against ischemic stroke with a XST-regulated stroke network analysis. Male Sprague Dawley rat model of MCAO and reperfusion were administered XST for 7 days while the control group was not treated. Three conditions were compared with three replicates each. These are: (1) sham; (2) model (3) XST treatment. Whole genome microarray analysis was performed using Affymetrix rat Genome 230 2.0 chips.

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Transcriptomics provides novel insights into the regulatory mechanism of panax notoginseng derived exosome-like nanoparticles on HUVECs cells

Project description:In current study, we observed that panax notoginseng derived exosome-like nanoparticles successfully promoted proliferation, significantly inhibited apoptosis and greatly facilitated migration in HUVECs, further highlighting the robust therapy effects of HIF1A-AS1 to cardiovascular diseases (CVD). Moreover, transcriptomics was implemented to uncover its underlying mechanism. A total of 276 differentially expressed genes (DEGs) were identified, with some of them enriched in apoptosis, migration and cell cycle related pathways. Intriguingly, some DEGs were annotated in vascular development or coagulation function pathways. In view of this, we suggested panax notoginseng derived exosome-like nanoparticles mediated the progression of CVD by not only regulating the function of HUVECs, but also altering vascular development or coagulation function. Lastly, RT-qPCR confirmed the veracity and reliability of RNA-sequencing results.

2025-05-16 | GSE203636 | GEO

Panax notoginseng

Project description:Panax notoginseng Transcriptome

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The effect of XUESAITONG on gene expression profile after focal cerebral ischemia in rats

2014-09-23 | GSE61616 | GEO

Phased secondary small interfering RNAs in Panax notoginseng

Project description:Recent results demonstrated that either non-coding or coding genes generate phased secondary small interfering RNAs (phasiRNAs) guided by specific miRNAs. Till now, there is no studies for phasiRNAs in Panax notoginseng (Burk.) F.H. Chen (P. notoginseng), an important traditional Chinese herbal medicinal plant species. Here we performed a genome-wide discovery of phasiRNAs and its host PHAS loci in P. notoginseng by analyzing small RNA sequencing profiles. Degradome sequencing profile was used to identify the trigger miRNAs of these phasiRNAs and potential targets of phasiRNAs. We also used RLM 5'-RACE to validate some of the identified phasiRNA targets. After analyzing 24 small RNA sequencing profiles of P. notoginseng, 204 and 90 PHAS loci that encoded 21 and 24 nucleotide (nt) phasiRNAs were identified. Furthermore, we found that phasiRNAs produced from some pentatricopeptide repeat-contain (PPR) genes target another layer of PPR genes as validated by both the degradome sequencing profile and RLM 5'-RACE analysis. We also find that miR171 with 21 nt triggers the 21 nt phasiRNAs from its conserved targets. We validated that some phasiRNAs generated from PPRs are functional by targeting other PPRs in trans. These results provide the first set of PHAS loci and phasiRNAs in P. notoginseng, and enhance our understanding of PHAS in plants.

2018-02-14 | GSE98118 | GEO

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