Systems Biology

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    Protocols in Current Issue
    A Molecular Cloning and Sanger Sequencing-based Protocol for Detecting Site-specific DNA Methylation
    Authors:  Wei Guo, Anthony Cannon and Damon Lisch, date: 05/05/2022, view: 475, Q&A: 0
    [Abstract]

    DNA methylation is a conserved chemical modification, by which methyl groups are added to the cytosine of DNA molecules. Methylation can influence gene expression without changing the sequence of a particular gene. This epigenetic effect is an intriguing phenomenon that has puzzled biologists for years. By probing the temporal and spatial patterns

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    circFL-seq, A Full-length circRNA Sequencing Method
    Authors:  Zelin Liu and Ence Yang, date: 04/20/2022, view: 779, Q&A: 1
    [Abstract]

    Due to overlapping sequences with linear cognates, identifying internal sequences of circular RNA (circRNA) remains a challenge. Recently, we have developed a full-length circRNA sequencing method (circFL-seq) and computational pipeline, to profile ordinary and fusion circRNA at the isoform level. Compared to short-read RNA-seq, rolling circular

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    Whole-genome Methylation Analysis of APOBEC Enzyme-converted DNA (~5 kb) by Nanopore Sequencing
    [Abstract]

    In recent years, DNA methylation research has been accelerated by the advent of nanopore sequencers. However, read length has been limited by the constraints of base conversion using the bisulfite method, making analysis of chromatin content difficult. The read length of the previous method combining bisulfite conversion and long-read sequencing

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    Enrichment of Tyrosine Phosphorylated Peptides for Quantitative Mass Spectrometry Analysis of RTK Signaling Dynamics
    Authors:  Vidyasiri Vemulapalli, Stephen C. Blacklow, Steven P. Gygi and Alison Erickson, date: 02/05/2022, view: 1098, Q&A: 0
    [Abstract]

    Cells sense and respond to mitogens by activating a cascade of signaling events, primarily mediated by tyrosine phosphorylation (pY). Because of its key roles in cellular homeostasis, deregulation of this signaling is often linked to oncogenesis. To understand the mechanisms underlying these signaling pathway aberrations, it is necessary to

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    Subcellular RNA-seq for the Analysis of the Dendritic and Somatic Transcriptomes of Single Neurons
    Authors:  Julio D. Perez and Erin M. Schuman, date: 01/05/2022, view: 1349, Q&A: 0
    [Abstract]

    In neurons, local translation in dendritic and axonal compartments allows for the fast and on-demand modification of the local proteome. As the last few years have witnessed dramatic advancements in our appreciation of the brain’s neuronal diversity, it is increasingly relevant to understand how local translation is regulated according to

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    TGIRT-seq Protocol for the Comprehensive Profiling of Coding and Non-coding RNA Biotypes in Cellular, Extracellular Vesicle, and Plasma RNAs
    Authors:  Hengyi Xu, Ryan M. Nottingham and Alan M. Lambowitz, date: 12/05/2021, view: 1170, Q&A: 0
    [Abstract]

    High-throughput RNA sequencing (RNA-seq) has extraordinarily advanced our understanding of gene expression and disease etiology, and is a powerful tool for the identification of biomarkers in a wide range of organisms. However, most RNA-seq methods rely on retroviral reverse transcriptases (RTs), enzymes that have inherently low fidelity and

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    Macroscopic Structural and Connectome Mapping of the Mouse Brain Using Diffusion Magnetic Resonance Imaging
    Authors:  Tanzil Mahmud Arefin, Choong Heon Lee, Jordon D. White, Jiangyang Zhang and Arie Kaffman, date: 11/20/2021, view: 1694, Q&A: 0
    [Abstract]

    Translational work in rodents elucidates basic mechanisms that drive complex behaviors relevant to psychiatric and neurological conditions. Nonetheless, numerous promising studies in rodents later fail in clinical trials, highlighting the need for improving the translational utility of preclinical studies in rodents. Imaging of small rodents

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    Histone modification ChIP-seq on Arabidopsis thaliana Plantlets
    Authors:  Juan S. Ramirez-Prado, David Latrasse and Moussa Benhamed, date: 11/05/2021, view: 1658, Q&A: 1
    [Abstract]

    Characterizing the molecular mechanisms regulating gene expression is crucial for understanding the regulatory processes underlying physiological responses to environmental and developmental signals in eukaryotes. The covalent modification of histones contributes to the compaction levels of chromatin, as well as the recruitment of the

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    Protocols to Induce, Prevent, and Treat Post-traumatic Stress Disorder-like Memory in Mice: Optogenetics and Behavioral Approaches
    [Abstract]

    One of the cardinal features of post-traumatic stress disorder (PTSD) is a paradoxical memory alteration including both emotional hypermnesia for salient trauma-related cues and amnesia for the surrounding traumatic context. Interestingly, some clinical studies have suggested that contextual amnesia would causally contribute to the PTSD-related

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    Protocol for RNA-seq Expression Analysis in Yeast
    Author:  Stefan Bohn, date: 09/20/2021, view: 1625, Q&A: 0
    [Abstract]

    Genome-wide sequencing of RNA (RNA-seq) has become an inexpensive tool to gain key insights into cellular and disease mechanisms. Sample preparation and sequencing are streamlined and allow the acquisition of hundreds of gene expression profiles in a few days; however, in particular, data processing, curation, and analysis involve numerous steps

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