Ontology highlight
ABSTRACT:
PROVIDER: PRJNA717318 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14088456_1.fastq.gz | Fastqsanger.gz | |||
| SRR14088456_2.fastq.gz | Fastqsanger.gz | |||
| SRR14088457_1.fastq.gz | Fastqsanger.gz | |||
| SRR14088457_2.fastq.gz | Fastqsanger.gz | |||
| SRR14088458_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
Similar Datasets
Project description:This study intends to explore the clinicopathological characteristics and survival prognosis of locally recurrent colorectal cancer patients with different treatment modes by retrospectively analyzing the medical records of locally recurrent colorectal cancer patients who received hospitalization in our center. Transcriptome sequencing and public databases were used to screen for molecular markers related to locally recurrent colorectal cancer and to explore molecular markers’ regulatory role in the progression of locally recurrent colorectal cancer.
| 116635 | ecrin-mdr-crc
Project description:Our goal was to investigate the transcriptional response of T. urticae to different Arabidopsis plants with varying levels of indole glucosinolates.
2013-11-25 | GSE48771 | GEO
Project description:BACKGROUND: The use of phytochemicals is a promising solution in biological control against salmon louse (Lepeophtheirus salmonis). Glucosinolates (Gls) belong to a diverse group of compounds used as protection against herbivores by plants in the Brassicaceae family, while in vertebrates, ingested glucosinolates exert health-promoting effects due to their antioxidant and detoxifying properties as well as effects on cell proliferation and growth. The aim of this study was to investigate if Atlantic salmon fed two different doses of glucosinolate-enriched feeds would be protected against lice infection. The effects of feeding high dose of glucosinolates before the infection, and of high and low doses 5 weeks into the infection were studied. METHODS: Skin was screened by 15k oligonucleotide microarray and qPCR. RESULTS: 25% reduction (p < 0.05) in lice counts was obtained in the low dose group and 17% reduction in the high dose group compared to fish fed control feed. Microarray analysis revealed induction of over 50 interferon (IFN)-related genes prior to lice infection. Genes upregulated 5 weeks into the infection in glucosinolate-enriched dietary groups included Type 1 pro-inflammatory factors, antimicrobial and acute phase proteins, extracellular matrix remodeling proteases and iron homeostasis regulators. In contrast, genes involved in muscle contraction, lipid and glucose metabolism were found more highly expressed in the skin of infected control fish. CONCLUSIONS: Atlantic salmon fed glucosinolates had a significantly lower number of sea lice at the end of the experimental challenge. Feeding glucosinolates coincided with increased expression of IFN-related genes, and higher expression profiles of Type 1 immune genes late into the infection. In addition, regulation of genes involved in the metabolism of iron, lipid and sugar suggested an interplay between metabolism of nutrients and mechanisms of resistance.
2016-03-19 | GSE79393 | GEO
Project description:We analyzed transcriptome changes from germinating cyp79B2 cyp79B3, qko, and pad3 mutant Arabidopsis seeds. Here were used mutant lines in Col-0 genetic background: a cyp79B2 cyp79B3 double mutant defective in indolic glucosinolate (cyp79B2/B3), a cyp79B2 cyp79B3 myb28 myb29 quadruple mutant defective in indolic and aliphatic glucosinolates (qko), and a camalexin deficient mutant (pad3). Differentially expressed genes were identified at 3, 6 and 10 days after sowing from both the mutant line seeds and from Alternaria brassicicola when inoculated seeds were analyzed.
2024-03-26 | GSE214602 | GEO
Project description:In order to more accurately discover the cause of drug resistance in tumor treatment, and to provide a new basis for precise treatment.
Therefore, based on the umbrella theory of precision medicine, we carried out this single-center, prospective, and observational study to include patients with liver metastases from colorectal cancer. By combining genome, transcriptome, and proteomic sequencing data, we established a basis for colorectal cancer liver Transfer the multi-omics data of the sample, describe the reason for the resistance of the first-line treatment, and search for new therapeutic targets.
| 2349788 | ecrin-mdr-crc
Project description:GelC-MS analysis of Naja naja snake venom that goes alongside a genome sequencing and transcriptome analysis of the Indian cobra.
2019-11-08 | MSV000084564 | MassIVE
Project description:Purpose: The goals of this study are to analyze the transcriptome of Arabidopsis thaliana treated after flg22 and to find changes of glucosinolate metabolism genes after treatment. Methods: Total mRNA of 10 day wild-type Arabidopsis seedlings that were treated with and without flg22( final concentrations 1μmol/L) in 1/2 MS medium for 4h, were extracted respectively. Each sample was harvested in three independent biological replicates with equal weight and mixed ,subsequently sequencing. The sequence reads that passed quality filters were mapped to the Arabidopsis_thaliana genome (TAIR10.18).Then the mapping genes were used for the abundance and functional analysis. Results: We mapped about 45 million and 52 million sequence reads of control sample and treatment sample to the Arabidopsis_thaliana genome (TAIR10.18) and identified total 23,413 genes with Botiw/TopHat workflow. Comparison of the two samples showed 1,200 differentially expressed genes (DEGs), including 290 down-regulated and 910 up-regulated genes. The DEGs were associated with energy metabolism, amino acid metabolism and biosynthesis of secondary metabolites. After flg22 treatment, genes involved in indolic glucosinolate biosynthesis pathway were up-regulated significantly，which is further demonstrated by Real Time RT-PCR, while aliphatic glucosinolate pathway almost had no change, indicating the important role of indolic glucosinolates in plant defense responses. Conclusion: Our study provides the overall genetic resource of Arabidopsis_thaliana after treated by flg22 to date. These data will pave the way for further studies about deeply understand pathogen induced defense and the contribution of indolic glucosinolates.
2017-03-22 | GSE56117 | GEO
Project description:Purpose: The goals of this study are to analyze the transcriptome of five time point in broccoli seed germination and sprout development and to find the putative glucosinolate metabolism genes in the stage. Methods: Total mRNA of germinated seeds, 3 day cotyledons, 7 day botyledons, 11 day cotyledons and 11 day euphyllas of wild-type broccoli were harvested. Each sample was harvested in three independent biological replicates with equal weight and subsequently pooled together for sequencing. The sequence reads that passed quality filters were de novo assembled using VELVET followed by OASES. Then the assembled unigenes were used for the abundance and functional analysis. Results: A total of ~85million 251bp reads were obtained. After de novo assembly and searching the assembled transcripts against the Arabidopsis thaliana and Nr databases, 19,441 top-hit transcripts were clustered as unigenes with an average length of 2,133bp. These unigenes were classified according to their putative functional categories. Cluster analysis of total unigenes with similar expression patterns and differentially expressed unigenes among different tissues,as well as transcription factor analysis were performed. We identified 25 putative glucosinolate metabolismgenes sharing 62.04-89.72% nucleotide sequence identity with the Arabidopsis orthologs. This established a broccoli glucosinolate metabolic pathway with high colinearity to Arabidopsis. Many of the biosynthetic and degradation genes showed higher expression after germination than in seeds; especially the expression of the myrosinaseTGG2 was 20-130 times higher.These results along with the previous reports that glucosinolate concentration decreased exponentially once after germination indicate the breakdown products of glucosinolates may play important roles in broccoli seed germination and sprout development. Conclusion: Our study provides the largest genetic resource of broccoli to date. These data will pave the way for further studies and genetic engineering of broccoli sprouts to develop functional vegetables containing high levels of the anticarcinogenic glucosinolates. They will also provide new insight into the genomic research of this species and its relatives. Wild-type broccoli mRNA profiles of seeds, 3 day cotyledons, 7 day botyledons, 11 day cotyledons and 11 day euphyllas were generated by deep sequencing, three biological replicates pooling together for each tissue, using Illumina Myseq platform.
2014-03-18 | E-GEOD-53298 | biostudies-arrayexpress
Project description:CYP83A1 and CYP83B1 are important enzymes in the biosynthesis of glucosinolates. However, only few of their interaction partners are known so far. We therefore performed a GFPtrap affinity enrichment using protein extracts from lines expressing tagged CYP83A1 or CYP83B1, or from wild type plants as background control.
2017-11-30 | PXD005585 | Pride
Project description:The transcriptional and metabolic profiles of rosettes of three independent Arabidopsis thaliana ecotype Wassiliewska lines overexpressing the soybean early noduline GmENOD40 gene were compared to those of wt, and a biomarker analysis was performed. ENOD40 overexpression resulted in 382 modulated genes, 142 of which upregulated and 165 downregulated in all the three transformed lines. Cell wall, membrane, hydrolase activity on glycosidic bonds, defense response and response to stimulus gene categories were overrepresented in the modulated genes compared to TAIR complete database. Metabolomics analysis (through liquid chromatography-mass spectrometry) allowed to putatively identify 13 different glucosinolates, some flavonoids, sinapic and ferulic acid derivatives, hydroxybenzoic acid derivatives, non aromatic organic acids, amino acids. Positive genes biomarkers of the transformed plants were mainly involved in cell wall turnover, whereas positive metabolite biomarkers were the methylthioalkyl-glucosinolates.
2015-05-08 | GSE37867 | GEO