Systems Biology

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    Protocols in Current Issue
    Low-cost and Multiplexable Whole mRNA-Seq Library Preparation Method with Oligo-dT Magnetic Beads for Illumina Sequencing Platforms
    Authors:  Makoto Kashima, Ayumi Deguchi, Ayumi Tezuka and Atsushi J. Nagano, date: 06/20/2020, view: 907, Q&A: 0
    [Abstract] RNA-Seq is a powerful method for transcriptome analysis used in varied field of biology. Although several commercial products and hand-made protocols enable us to prepare RNA-Seq library from total RNA, their cost are still expensive. Here, we established a low-cost and multiplexable whole mRNA-Seq library preparation method for illumine ...
    HIV-CRISPR: A CRISPR/Cas9 Screening Method to Identify Genes Affecting HIV Replication
    Authors:  Ferdinand Roesch and Molly OhAinle, date: 05/05/2020, view: 720, Q&A: 0
    [Abstract] Screening with CRISPR/Cas9 technology has already led to significant discoveries in the fields of cancer biology, cell biology and virology. Because of the relatively low false discovery rates and the ability to perform high-throughput, pooled approaches, it has rapidly become the assay of choice for screening studies, including whole-genome ...
    Sequence Alignment Using Machine Learning for Accurate Template-based Protein Structure Prediction
    Authors:  Shuichiro Makigaki and Takashi Ishida, date: 05/05/2020, view: 812, Q&A: 0
    [Abstract] Template-based modeling, the process of predicting the tertiary structure of a protein by using homologous protein structures, is useful when good templates can be available. Indeed, modern homology detection methods can find remote homologs with high sensitivity. However, the accuracy of template-based models generated from the ...
    Circadian Gene Profiling in Laser Capture Microdissected Mouse Club Cells
    Authors:  Zhenguang Zhang and Andrew Loudon, date: 04/20/2020, view: 619, Q&A: 0
    [Abstract] Cell heterogeneity is high in tissues like lung. Research conducted on pure population of cells usually offers more insights than bulk tissues, such as circadian clock work. In this protocol, we provide a detailed work flow on how to do circadian clock study by RNA seq in laser capture micro-dissected mouse lung club cells. The method uses frozen ...
    Experiments for in silico evaluation of Optimality of Photosynthetic Nitrogen Distribution and Partitioning in the Canopy: an Example Using Greenhouse Cucumber Plants
    Authors:  Yi-Chen Pao, Tsu-Wei Chen, Dany Pascal Moualeu-Ngangue and Hartmut Stützel, date: 03/20/2020, view: 800, Q&A: 0
    [Abstract] Acclimation of leaf traits to fluctuating environments is a key mechanism to maximize fitness. One of the most important strategies in acclimation to changing light is to maintain efficient utilization of nitrogen in the photosynthetic apparatus by continuous modifications of between-leaf distribution along the canopy depth and within-leaf ...
    Delayed Alternation Task for the Study of Spatial Working and Long Term Memory in Rats
    Authors:  Megi Hoxha and Marta Sabariego, date: 03/05/2020, view: 927, Q&A: 0
    [Abstract] Memory systems can hold previously presented information for several seconds, bridging gaps between discontinuous events. It has been previously demonstrated that the hippocampus and the medial entorhinal cortex (mEC) are necessary for memory retention over delay intervals in alternation tasks. Here we describe the delayed alternation task, a ...
    mRNA Extraction from Gill Tissue for RNA-sequencing
    Authors:  Jukka-Pekka Verta and Felicity Jones, date: 03/05/2020, view: 738, Q&A: 0
    [Abstract] Adaptation is thought to proceed in part through spatial and temporal changes in gene expression. Fish species such as the threespine stickleback are powerful vertebrate models to study the genetic architecture of adaptive changes in gene expression since divergent adaptation to different environments is common, they are abundant and easy to study ...
    ChIP-Seq from Limited Starting Material of K562 Cells and Drosophila Neuroblasts Using Tagmentation Assisted Fragmentation Approach
    Authors:  Junaid Akhtar, Piyush More and Steffen Albrecht, date: 02/20/2020, view: 673, Q&A: 0
    [Abstract] Chromatin immunoprecipitation is extensively used to investigate the epigenetic profile and transcription factor binding sites in the genome. However, when the starting material is limited, the conventional ChIP-Seq approach cannot be implemented. This protocol describes a method that can be used to generate the chromatin profiles from as low as ...
    Mapping the Mechanome–A Protocol for Simultaneous Live Imaging and Quantitative Analysis of Cell Mechanoadaptation and Ingression
    [Abstract] Mechanomics, the mechanics equivalent of genomics, is a burgeoning field studying mechanical modulation of stem cell behavior and lineage commitment. Analogous to mechanical testing of a living material as it adapts and evolves, mapping of the mechanome necessitates the development of new protocols to assess changes in structure and function in ...
    Isolation and Quantification of Metabolite Levels in Murine Tumor Interstitial Fluid by LC/MS
    Authors:  Mark R Sullivan, Caroline A Lewis and Alexander Muir, date: 11/20/2019, view: 2242, Q&A: 0
    [Abstract] Cancer is a disease characterized by altered metabolism, and there has been renewed interest in understanding the metabolism of tumors. Even though nutrient availability is a critical determinant of tumor metabolism, there has been little systematic study of the nutrients directly available to cancer cells in the tumor microenvironment. Previous ...



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