Systems Biology

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    Protocols in Current Issue
    Proteome Integral Solubility Alteration (PISA) Assay in Mammalian Cells for Deep, High-Confidence, and High-Throughput Target Deconvolution

    Chemical proteomics focuses on the drug–target–phenotype relationship for target deconvolution and elucidation of the mechanism of action—key and bottleneck in drug development and repurposing. Majorly due to the limits of using

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    Efficient Generation of Genome-wide Libraries for Protein–ligand Screens Using Gibson Assembly
    Authors:  Tamara Sternlieb, Mira Loock, Mengjin Gao and Igor Cestari, date: 11/20/2022, view: 487, Q&A: 0

    Genome-wide screens using yeast or phage displays are powerful tools for identifying protein–ligand interactions, including drug or vaccine targets, ligand receptors, or protein–protein interactions. However, assembling libraries

    ...
    Proteome Integral Solubility Alteration (PISA) Assay in Mammalian Cells for Deep, High-Confidence, and High-Throughput Target Deconvolution
    [Abstract]

    Chemical proteomics focuses on the drug–target–phenotype relationship for target deconvolution and elucidation of the mechanism of action—key and bottleneck in drug development and repurposing. Majorly due to the limits of using chemically modified ligands in affinity-based methods, new, unbiased, proteome-wide, and MS-based

    ...
    Efficient Generation of Genome-wide Libraries for Protein–ligand Screens Using Gibson Assembly
    Authors:  Tamara Sternlieb, Mira Loock, Mengjin Gao and Igor Cestari, date: 11/20/2022, view: 487, Q&A: 0
    [Abstract]

    Genome-wide screens using yeast or phage displays are powerful tools for identifying protein–ligand interactions, including drug or vaccine targets, ligand receptors, or protein–protein interactions. However, assembling libraries for genome-wide screens can be challenging and often requires unbiased cloning of 105–107 DNA

    ...
    ATAC-Seq of a Single Myofiber from Mus musculus
    Authors:  Korin Sahinyan, Darren M. Blackburn and Vahab D. Soleimani, date: 06/20/2022, view: 2051, Q&A: 0
    [Abstract]

    Chromatin accessibility is a key determinant of gene expression that can be altered under different physiological and disease conditions. Skeletal muscle is made up of myofibers that are highly plastic and adaptive. Therefore, assessing the genome-wide chromatin state of myofibers under various conditions is very important to gain insight into the

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    Protocol for Initiating and Monitoring Bumble Bee Microcolonies with Bombus impatiens (Hymenoptera: Apidae)
    Author:  David M. Lehmann, date: 06/20/2022, view: 1726, Q&A: 0
    [Abstract]

    Populations of some bumble bee species are in decline, prompting the need to better understand bumble bee biology and for assessing the effects of environmental stressors on these important pollinators. Microcolonies have been successfully used for investigating a range of endpoints, including behavior, gut microbiome, nutrition, development,

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    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: 1460, Q&A: 1
    [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: 1765, 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: 1798, 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: 2323, 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: 2267, 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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