Systems Biology


    Protocols in Current Issue
    Trypanosomatid, fluorescence-based in vitro U-insertion/U-deletion RNA-editing (FIDE)
    Authors:  Wolf-Matthias Leeder, Elisabeth Kruse and H. Ulrich Göringer, date: 03/05/2021, view: 1647, Q&A: 0

    Gene expression within the mitochondria of African trypanosomes and other protozoan organisms relies on a nucleotide-specific RNA-editing reaction. In the process exclusively uridine (U)-nucleotides are site-specifically inserted into and deleted from sequence-deficient primary transcripts to convert them into translatable mRNAs. The reaction is

    Primer ID Next-Generation Sequencing for the Analysis of a Broad Spectrum Antiviral Induced Transition Mutations and Errors Rates in a Coronavirus Genome

    Next generations sequencing (NGS) has become an important tool in biomedical research. The Primer ID approach combined with the MiSeq platform overcomes the limitation of PCR errors and reveals the true sampling depth of population sequencing, making it an ideal tool to study mutagenic effects of potential broad-spectrum antivirals on RNA viruses.

    EmPC-seq: Accurate RNA-sequencing and Bioinformatics Platform to Map RNA Polymerases and Remove Background Error

    Transcription errors can substantially affect metabolic processes in organisms by altering the epigenome and causing misincorporations in mRNA, which is translated into aberrant mutant proteins. Moreover, within eukaryotic genomes there are specific Transcription Error-Enriched genomic Loci (TEELs) which are transcribed by RNA polymerases with

    Low-cost and High-throughput RNA-seq Library Preparation for Illumina Sequencing from Plant Tissue
    Authors:  Marta Bjornson, Kaisa Kajala, Cyril Zipfel and Pingtao Ding, date: 10/20/2020, view: 3208, Q&A: 0
    [Abstract] Transcriptome analysis can provide clues to biological processes affected in different genetic backgrounds or/and under various conditions. The price of RNA sequencing (RNA-seq) has decreased enough so that medium- to large-scale transcriptome analyses in a range of conditions are feasible. However, the price and variety of options for library ...
    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: 4121, 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: 4692, 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: 3154, 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: 2345, 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 ...
    mRNA Extraction from Gill Tissue for RNA-sequencing
    Authors:  Jukka-Pekka Verta and Felicity Jones, date: 03/05/2020, view: 2427, 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 ...
    Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq
    [Abstract] Most nematodes are small worms that lack enough RNA for regular RNA-seq protocols without pooling hundred to thousand of individuals. We have adapted the Smart-seq2 protocol in order to sequence the transcriptome of an individual worm. While developed for individual Steinernema carpocapsae and Caenorhabditis elegans larvae as ...

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