Identification of Brassinosteroid Target Genes by Chromatin Immunoprecipitation Followed by High-Throughput Sequencing (ChIP-seq) and RNA-Sequencing

2017 ◽  
pp. 63-79 ◽  
Author(s):  
Trevor Nolan ◽  
Sanzhen Liu ◽  
Hongqing Guo ◽  
Lei Li ◽  
Patrick Schnable ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
High Throughput ◽  
Chromatin Immunoprecipitation ◽  
High Throughput Sequencing ◽  
Target Genes

Multilocus sequence typing of Salmonella strains by high-throughput sequencing of selectively amplified target genes

2012 ◽  
Vol 88 (1) ◽  
pp. 127-133 ◽  
Author(s):  
Pallavi Singh ◽  
Steven L. Foley ◽  
Rajesh Nayak ◽  
Young Min Kwon
Keyword(s):  
High Throughput ◽  
Multilocus Sequence Typing ◽  
High Throughput Sequencing ◽  
Target Genes

scholarly journals Identification of Exogenous Nitric Oxide-Responsive miRNAs from Alfalfa (Medicago sativa L.) under Drought Stress by High-Throughput Sequencing

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 30
Author(s):  
Yaodong Zhao ◽  
Wenjing Ma ◽  
Xiaohong Wei ◽  
Yu Long ◽  
Ying Zhao ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Drought Stress ◽  
Medicago Sativa ◽  
High Throughput ◽  
Drought Resistance ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Medicago Sativa L

Alfalfa (Medicago sativa L.) is a high quality leguminous forage. Drought stress is one of the main factors that restrict the development of the alfalfa industry. High-throughput sequencing was used to analyze the microRNA (miRNA) profiles of alfalfa plants treated with CK (normal water), PEG (polyethylene glycol-6000; drought stress), and PEG + SNP (sodium nitroprusside; nitric oxide (NO) sprayed externally under drought stress). We identified 90 known miRNAs belonging to 46 families and predicted 177 new miRNAs. Real-time quantitative fluorescent PCR (qRT-PCR) was used to validate high-throughput expression analysis data. A total of 32 (14 known miRNAs and 18 new miRNAs) and 55 (24 known miRNAs and 31 new miRNAs) differentially expressed miRNAs were identified in PEG and PEG + SNP samples. This suggested that exogenous NO can induce more new miRNAs. The differentially expressed miRNA maturation sequences in the two treatment groups were targeted by 86 and 157 potential target genes, separately. The function of target genes was annotated by gene ontology (GO) enrichment and kyoto encyclopedia of genes and genomes (KEGG) analysis. The expression profiles of nine selected miRNAs and their target genes verified that their expression patterns were opposite. This study has documented that analysis of miRNA under PEG and PEG + SNP conditions provides important insights into the improvement of drought resistance of alfalfa by exogenous NO at the molecular level. This has important scientific value and practical significance for the improvement of plant drought resistance by exogenous NO.

scholarly journals Analysis of the Differential Exosomal miRNAs of DC2.4 Dendritic Cells Induced by Toxoplasma gondii Infection

2019 ◽  
Vol 20 (21) ◽  
pp. 5506
Author(s):  
Dong-Liang Li ◽  
Wei-Hao Zou ◽  
Sheng-Qun Deng ◽  
Hong-Juan Peng
Keyword(s):  
Dendritic Cells ◽  
Toxoplasma Gondii ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Quantitative Polymerase Chain Reaction ◽  
Biologically Active ◽  
Transferase Activity ◽  
Bioinformatics Analyses ◽  
Exosomal Mirnas

Toxoplasma gondii is an intracellular parasite that infects humans and other warm-blooded animals. Exosomes are endocytic-derived vesicles released by cells, representing an important mode of intercellular communication. In exosomes, specific molecules of proteins, lipids, and mRNAs or miRNAs have been detected, some of which are capable of transferring biologically active molecules to recipient cells. Dendritic cells (DCs) are the only antigen-presenting cells (APCs) that activate the initial immune response. In this study, high-throughput sequencing was used to analyze the exosomal miRNA profile of DC2.4 cells infected with Toxoplasma gondii for 28 h, compared with those of uninfected DC2.4 cells. Differential exosomal miRNAs (DEmiRs) from these two cell groups were analyzed. Through high-throughput sequencing, 3434 DEmiRs were obtained, and 12 stably enriched DEmiRNAs were verified by Reverse Transcription-quantitative Polymerase Chain Reaction (RT-qPCR) and selected for further analysis. The target genes of these 12 miRNAs were predicted with online analysis software and subjected to bioinformatics analyses including protein–protein interaction (PPI) network analysis, key driver analysis (KDA), gene ontology (GO) enrichment, and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. These DEmiRs were found to be associated with a variety of biological processes and signaling pathways involved in host ubiquitin system, innate immunity, biosynthesis, and transferase activity and could be potential biomarkers for T. gondii infection.

scholarly journals Pathology tissue-chromatin immunoprecipitation, coupled with high-throughput sequencing, allows the epigenetic profiling of patient samples

2010 ◽  
Vol 107 (50) ◽  
pp. 21535-21540 ◽  
Author(s):  
M. Fanelli ◽  
S. Amatori ◽  
I. Barozzi ◽  
M. Soncini ◽  
R. Dal Zuffo ◽  
...  
Keyword(s):  
High Throughput ◽  
Chromatin Immunoprecipitation ◽  
High Throughput Sequencing

scholarly journals The Effect of Different Pollination on the Expression of Dangshan Su Pear MicroRNA

2017 ◽  
Vol 2017 ◽  
pp. 1-18 ◽  
Author(s):  
Xi Cheng ◽  
Chongchong Yan ◽  
Jinyun Zhang ◽  
Chenhui Ma ◽  
Shumei Li ◽  
...  
Keyword(s):  
High Throughput ◽  
Fruit Quality ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Cell Content ◽  
Qrt Pcr ◽  
Stone Cell ◽  
Negative Effect

The high-throughput sequencing of pear “Dangshan Su” × “Yali” (whose fruits lignin and stone cell content are high and quality is poor) and pear “Dangshan Su” × “Wonhwang” (whose fruits with low content of lignin and stone cell and the quality are better ) found that the expressions of these two miRNAs (pyr-1809 and pyr-novel-miR-144-3p) were significantly different; their corresponding target genes encode two kinds of laccase (Pbr018935.1 and Pbr003857.1). qRT-PCR results showed that these two enzymes are involved in the formation of lignin and stone cells and the existence of these two miRNAs has a negative effect on them. It was concluded that the effect of pollination on the development of stone cells may affect the synthesis of lignin, through the regulation of laccase controlled by miRNAs, and ultimately affect the formation of stone cell and fruit quality.

Sign in / Sign up

Export Citation Format

Share Document