Có 20+ tài liệu thuộc chủ đề "High-throughput sequencing"
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Background: Studies on the airway microbiome have been performed using a wide range of laboratory protocols for high-throughput sequencing of the bacterial 16S ribosomal RNA (16S rRNA) gene. We sought to determine the impact of number of polymerase chain reaction (PCR) steps (1- or 2- steps) and choice of target marker gene region (V3 V4 and V4) on the presentation...
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However, the current high- throughput DNA barcoding methods cannot obtain full-length barcode sequences due to read length limitations (e.g. We present a bioinformatic pipeline, HIFI-SE, that takes reads generated from the 5 ′ and 3 ′ ends of the COI barcode region and assembles them into full-length barcodes. HIFI-SE is written in Python and includes four function modules of filter,...
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Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling. Background: Elucidation of immune populations with single-cell RNA-seq has greatly benefited the field of immunology by deepening the characterization of immune heterogeneity and leading to the discovery of new subtypes. However, single-cell methods inherently suffer from limitations in the recovery of complete. Results: Here, we systematically benchmarked seven high-throughput...
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We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. Environ- mental DNA molecules in the soil matrix the ancient sample was recovered from can easily overwhelm the small amounts of endogenous DNA. This is also true for DNA from people who collected and handled the sam- ples...
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High-throughput sequencing of circRNAs reveals novel insights into mechanisms of nigericin in pancreatic cancer. Results: In this study, a total of 183 common differentially expressed circRNAs were identified, and the reliability and validity of the sequencing data were verified by the PCR analysis. According to the parental genes of circRNAs, the GO analysis was performed to predict the most enriched...
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sequencing reveal respective roles of cold- related microRNAs across Chinese wild. Background: Chinese wild grapevine (Vitis amurensis) has remarkable cold stress tolerance, exceeding that of the common cultivated grapevine (Vitis vinifera L.).. Result: Here, we surveyed the expression dynamics of microRNAs (miRNAs) across Chinese wild grapevine (cv. Cabernet Sauvignon) under cold stress using high-throughput sequencing. The expression of some miRNAs...
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Understanding the liver under heat stress with statistical learning: an integrated. Background: We present results from a computational analysis developed to integrate transcriptome and metabolomic data in order to explore the heat stress response in the liver of the modern broiler chicken. Heat stress is a significant cause of productivity loss in the poultry industry, both in terms of increased...
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We identified 592 putative targets of the conserved miRNAs or tasiRNAs that showed significant accumulations of degradome reads. Conclusions: These results significantly enhanced our knowledge of the miRNAs and phasiRNAs, as well as their potential functions, in R. Full list of author information is available at the end of the article. 2019 Open Access This article is distributed under the...
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Full list of author information is available at the end of the article. 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. Despite these advantages, one of the technical challenges encountered with respect to metagenomic sequencing is obtaining adequate depth and breadth of coverage from pathogens like RNA vi- ruses...
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Results: Here we present a method, MiCoP (Microbiome Community Profiling), that uses fast-mapping of reads to build a comprehensive reference database of full genomes from viruses and eukaryotes to achieve maximum read usage and enable the analysis of the virome and eukaryome in each sample. Full list of author information is available at the end of the article. 2019 Open...
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Background: The mechanism of latency and the ability of the cyprinid herpesvirus 3 (CyHV-3) to establish life-long infections in carp remains poorly understood. Results: We demonstrated the changed expression of 27 miRNAs in the clinical phase and 5 in the latent phase of infection. Conclusions: The results of our analysis expand the knowledge of common carp microRNAs engaged during CyHV-3...
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Characterization of the chicken T cell. However, a comprehensive characterization of the TCRγδ repertoire is still missing in chicken.. Methods: In this study, we first obtained the detailed genomic organization of the TCRγ locus of chicken based on the latest assembly of the red jungle fowl genome sequences (GRCg6a) and then characterized the TCRγ repertoire in the thymus of four...
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Nevertheless, the process of sperm capacitation remains poorly understood and requires further elucidation. In the current study, via high throughput sequencing, we identified and explored the differentially expressed microRNAs (miRNAs) and mRNAs involved in boar sperm capacitation.. Results: We identified a total of 5342 mRNAs and 204 miRNAs that were differentially expressed in fresh and capacitated boar sperms. From these,...
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Besides proteins, microRNA (miRNA) is another important functional component of exosomes. We hypothesized that the miRNA profile of exosomes may change following EMT and these exosomal miRNAs may in return promote EMT, migration and invasion of cancer cells.. Results: The small RNA profile of exosomes was altered following EMT. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that...
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Chromosome aneuploidy was observed in both groups but was more frequent in CL-SL. Genes encoding amastins were present in higher copy numbers in VL-SL and CL-PR as well as being among predicted pseudogenes in CL-SL. Both chromosome and SNP profiles showed CL-SL and VL-SL to form two distinct groups. Full list of author information is available at the end of...