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  1. No Access

    Protocol

    Single-Cell Imaging of mRNA by Target RNA-Initiated RCA

    We present a powerful method for direct mRNA detection based on ligation-based recognition and in situ amplification, capable of single-cell imaging mRNA at single-nucleotide and single-molecule resolution. At...

    **aojun Ren, Yifan Wu, Ruijie Deng, **ghong Li in RNA Amplification and Analysis (2024)

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    Protocol

    Repurposing Decellularized Lung to Generate Vascularized Fat

    Conventional therapies to address critically sized defects in subcutaneous adipose tissue remain a reconstructive challenge for surgeons, largely due to the lack of graft pre-vascularization. Adipose tissue re...

    Lindsey K. Huff, Zihan Ling, Megan K. DeBari, ** Ren in Adipose-Derived Stem Cells (2024)

  3. No Access

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    Noninvasive Visualization of Amyloid-Beta Deposits in Alzheimer’s Amyloidosis Mice via Fluorescence Molecular Tomography Using Contrast Agent

    Alzheimer’s disease is pathologically featured by the accumulation of amyloid-beta (Aβ) plaque and neurofibrillary tangles. Compared to small animal positron emission tomography, optical imaging features nonio...

    Wuwei Ren, Ruiqing Ni in Biomarkers for Alzheimer’s Disease Drug Development (2024)

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    Protocol

    Simple N-Glycan Profile Analysis Using Lectin Staining, Mass Spectrometry, and GlycoMaple

    The Golgi apparatus is one of the major sites of protein and lipid glycosylation and processing. Protein N-glycosylation plays critical roles in protein folding, transport, stability, and activity. Various gly...

    Wei-Wei Ren, Morihisa Fujita in Golgi (2023)

  5. No Access

    Protocol

    Actin: Static and Dynamic Studies

    The actin cytoskeleton is a highly dynamic network in plant cells, which is precisely regulated by numerous actin-binding proteins. Hence, characterizing the biochemical activities of actin-binding proteins is...

    Huaqiang Ruan, Sha Zhang, Yi Zhang, Haiyun Ren in The Plant Cytoskeleton (2023)

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    Staining Starch with Iodine Solution

    Starch is important material in plant tissues, especially for storage tissues. Starches from different plant resources or tissues vary in morphology, content, and physicochemical properties. Starch and iodine ...

    Shengnan Zhao, Yinhui Ren, Cunxu Wei in Histochemistry of Single Molecules (2023)

  7. No Access

    Protocol

    Methods to Visualize and Quantify Cortical Microtubule Arrays in Arabidopsis Conical Cells

    Many studies from different model organisms have demonstrated that microtubules are essential for various cellular processes, including cell division, cell morphogenesis, and intracellular trafficking. In inte...

    **e Dang, Lilan Zhu, Huibo Ren, Deshu Lin in The Plant Cytoskeleton (2023)

  8. No Access

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    Protoplast Isolation for Plant Single-Cell RNA-seq

    The growth and development of plants depends on diversified gene expression in different cell types. Compared to traditional bulk RNA sequencing, droplet-based single-cell RNA sequencing (scRNA-seq) allows for...

    Shulin Ren, Ying Wang in Flower Development (2023)

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    High-Throughput Screening for Thermostable Polyester Hydrolases

    Due to the promise of more sustainable recycling of plastics through biocatalytic degradation, the search for and engineering of polyester hydrolases have become a thriving field of research. Furthermore, amon...

    Yannick Branson, Christoffel P. S. Badenhorst, Lara Pfaff, Carolin Buchmann in Metagenomics (2023)

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    Protocol

    Methylome Imputation by Methylation Patterns

    DNA methylation is studied extensively for its relations with several biological processes such as transcriptional regulation. While methylation levels are usually estimated per cytosine or genomic region, add...

    Ya-Ting Sabrina Chang, Ming-Ren Yen in Computational Epigenomics and Epitranscrip… (2023)

  11. No Access

    Protocol

    Quantifying the Binding and Target-Search Kinetics of Transcriptional Regulatory Factors by Live-Cell Single-Molecule Tracking

    Eukaryotic transcriptional regulatory factors, such as transcription factors and epigenetic regulatory factors, must locate, bind, and assemble at specific genomic regions to execute functions within the compl...

    Steven Ingersoll, Kyle Brown, Brian Ma, **aojun Ren in DNA-Protein Interactions (2023)

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    Synthetic Biology Meets Machine Learning

    This chapter outlines the myriad applications of machine learning (ML) in synthetic biology, specifically in engineering cell and protein activity, and metabolic pathways. Though by no means comprehensive, the...

    Brendan Fu-Long Sieow, Ryan De Sotto in Computational Biology and Machine Learning… (2023)

  13. No Access

    Protocol

    PAM-Less CRISPR-SpRY Genome Editing in Plants

    Engineered SpCas9 variant, SpRY, has been demonstrated to facilitate protospacer adjacent motif (PAM) unrestricted targeting of genomic DNA in various biological systems. Here we describe fast, efficient, and ...

    Simon Sretenovic, Xu Tang, Qiurong Ren, Yong Zhang, Yi** Qi in Plant Genome Engineering (2023)

  14. No Access

    Protocol

    Single-Cell Joint Profiling of Open Chromatin and Transcriptome by Paired-Seq

    Simultaneous detection of chromatin accessibility and transcription from the same cells promises to greatly facilitate the dissection of cell-type-specific gene regulatory programs in complex tissues. Paired-s...

    Chenxu Zhu, Zhaoning Wang, Bing Ren in Chromatin Accessibility (2023)

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    Protocol

    The Implication of Liquid Biopsy in the Non-small Cell Lung Cancer: Potential and Expectation

    Nowadays, lung cancer has remained the most lethal cancer, despite great advances in diagnosis and treatment. However, a large proportion of patients were diagnosed with locally advanced or metastatic disease ...

    Jianghao Ren, Ruijun Liu in Liquid Biopsies (2023)

  16. No Access

    Protocol

    Tissue Cultivation, Preparation, and Extraction of High Molecular Weight DNA for Single-Molecule Genome Sequencing of Plant-Associated Fungi

    Extraction of high-quality, high molecular weight DNA is a critical step for sequencing an organism’s genome. For fungi, DNA extraction is often complicated by co-precipitation of secondary metabolites, the mo...

    Laure Fauchery, Maxim Koriabine, Lillian P. Moore in Microbial Environmental Genomics (MEG) (2023)

  17. No Access

    Protocol

    Establishment of Embryonic Zebrafish Xenograft Assays to Investigate TGF-β Family Signaling in Human Breast Cancer Progression

    Transforming growth factor-β (TGF-β) family members have pivotal functions in controlling breast cancer progression, acting not only on cancer cells but also on other cells within the tumor microenvironment. H...

    Chao Li, ** Ma, Arwin Groenewoud, Jiang Ren, Sijia Liu in TGF-Beta Signaling (2022)

  18. No Access

    Protocol

    Real-Time Quantification of Cell Internalization Kinetics by Bioluminescent Probes

    Alongside the intracellular transport of nutrients needed for cellular homeostasis, great efforts exist to effectively deliver substances such as proteins and genes into the cell for therapy, gene editing, dis...

    Roxanne Castillo, Di Wu, Zheng Cao, Ran Yan, Kalea Fajardo, Jie Ren in Bioluminescence (2022)

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    Protocol

    In Situ Imaging of mRNA Splicing Variants by SpliceRCA

    We present a method for multiplexed in situ imaging of individual RNA splicing variants. This method enables quantifying RNA splicing variants with single-molecule resolution, discriminating splicing isoforms ...

    **aojun Ren, **ghong Li in Alternative Splicing (2022)

  20. No Access

    Protocol

    Quantification of Site-Specific 5-Formylcytosine by Integrating Peptide Nucleic Acid-Clamped Ligation with Loop-Mediated Isothermal Amplification

    The precise sensing of 5-formylcytosine (5fC) is of great significance because 5fC not only determines the nucleosome organization that regulates gene expression but also acts as a potential epigenetic marker ...

    Zhenhao Zhang, Weimin Tian, Wei Ren, Zheng** Li in DNA Modification Detection Methods (2022)

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