New Development and Application of Next Generation Sequencing

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: closed (21 July 2023) | Viewed by 2324

Special Issue Editors


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Guest Editor
Department of Biomedical Data Sciences, Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
Interests: next generation sequencing; sequencing; NGS data analysis; transcriptomics; genomics; bioinformatics and computational biology

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Guest Editor
Clinical Bioinformatics, Department of Pathology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
Interests: bioinformatics; next generation sequencing; genomics; bioinformatics and computational biology

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Guest Editor
1. Faculty of Science, Technology, Engineering & Mathematics, The Open University, Milton Keynes, UK
2. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
Interests: bioinformatics; next generation sequencing; single-cell biology

Special Issue Information

Dear Colleagues,

In the past 10-15 years, the next-generation sequencing (NGS) technologies have revolutionized many fields in biology and medicine. In human genomics, the $1000 genome goal has been achieved and now technology industries are aiming to get a human WGS under $100. This further drastically reduced sequencing cost together with international projects such as 1+Million Genomes Initiative have demanded new experimental and computational methods and FAIR data infrastructure in order to tackle this next wave of data tsunami. Besides the population scale expansion, we are also deepening our understanding at the individual level thanks to the fast adoption of single cell sequencing technology. Projects like Human Cell Atlas are linking researchers around the world to share and integrate tissue and organ profiles at single cell level to answer crucial fundamental questions in cancer genetics, neurology, stem cell based treatment, etc. Furthermore, in the areas of plant, animal and microbiome, new long read sequencing technologies and gene editing toolings are being applied routinely to provide unprecedented insight to move the science forward.

In this special issue, we encourage researchers to submit unpublished research work addressing new development and application of NGS including the following but not limited to:

  • NGS based disease prediction
  • Personalized cancer treatment
  • Single cell transcriptomic and spatial transcriptomics
  • Virus detection and classification
  • Gene modification using CRISPR/Cas9
  • Plant genomics
  • Metagenomics

Dr. Hailiang Mei
Dr. Andrew P. Stubbs
Dr. Wendi Bacon
Guest Editors

Manuscript Submission Information

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Keywords

  • NGS based disease prediction
  • personalized cancer treatment
  • single cell transcriptomic and spatial
  • virus detection and classification
  • gene modification using CRISPR/Cas9
  • plant genomics
  • metagenomics
 

Published Papers (1 paper)

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Research

19 pages, 10522 KiB  
Article
Comparative Transcriptome Profiles of Human HaCaT Cells in Response to Gynostemma pentaphyllum Extracts Obtained Using Three Independent Methods by RNA Sequencing
by Won Kyong Cho, Seung Hye Paek, Soo-Yun Kim, Sung Joo Jang, Sak Lee, Hoseong Choi, Yeonhwa Jo, Jeong Hun Lee and Sang Hyun Moh
Life 2023, 13(2), 423; https://doi.org/10.3390/life13020423 - 2 Feb 2023
Cited by 1 | Viewed by 1946
Abstract
Gynostemma pentaphyllum (GP) is widely used in herbal medicine. In this study, we developed a method for the large-scale production of GP cells using plant tissue culture techniques combined with bioreactors. Six metabolites (uridine, adenosine, guanosine, tyrosine, phenylalanine, and tryptophan) were identified in [...] Read more.
Gynostemma pentaphyllum (GP) is widely used in herbal medicine. In this study, we developed a method for the large-scale production of GP cells using plant tissue culture techniques combined with bioreactors. Six metabolites (uridine, adenosine, guanosine, tyrosine, phenylalanine, and tryptophan) were identified in GP extracts. Transcriptome analyses of HaCaT cells treated with GP extracts using three independent methods were conducted. Most differentially expressed genes (DEGs) from the GP-all condition (combination of three GP extracts) showed similar gene expression on treatment with the three individual GP extracts. The most significantly upregulated gene was LTBP1. Additionally, 125 and 51 genes were upregulated and downregulated, respectively, in response to the GP extracts. The upregulated genes were associated with the response to growth factors and heart development. Some of these genes encode components of elastic fibers and the extracellular matrix and are associated with many cancers. Genes related to folate biosynthesis and vitamin D metabolism were also upregulated. In contrast, many downregulated genes were associated with cell adhesion. Moreover, many DEGs were targeted to the synaptic and neuronal projections. Our study has revealed the functional mechanisms of GP extracts’ anti-aging and photoprotective effects on the skin using RNA sequencing. Full article
(This article belongs to the Special Issue New Development and Application of Next Generation Sequencing)
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