Cell Biology


    Protocols in Current Issue
    circFL-seq, A Full-length circRNA Sequencing Method
    Authors:  Zelin Liu and Ence Yang, date: 04/20/2022, view: 794, Q&A: 1

    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

    Fluidigm Based Single-cell Gene Expression Library Preparation from Patient-derived Small Intestinal Organoids
    Authors:  Kohei Suzuki and Ryuichi Okamoto, date: 10/05/2020, view: 2516, Q&A: 0
    [Abstract] In this protocol, we describe our methods to isolate crypts from patients' biopsy samples and to culture human intestinal stem cells as it’s called “organoid.” Beyond that, we describe how to dissociate organoids cells into single cells for single-cell analysis as a further application. This protocol should provide investigators sufficient tools ...
    Ex vivo Culture Assay Using Human Hair Follicles to Study Circadian Characteristics
    Authors:  Atsuhiro Nishida, Yoshiki Miyawaki, Koichi Node and Makoto Akashi, date: 06/05/2020, view: 2270, Q&A: 0
    [Abstract] Ex vivo culture assays of biopsy specimens are advantageous for the experimental evaluation of human circadian characteristics. We developed a simple and non-invasive experimental evaluation method for monitoring the expression of circadian clock genes in an ex vivo culture assay using human hair follicles. This method imposes ...
    Circadian Gene Profiling in Laser Capture Microdissected Mouse Club Cells
    Authors:  Zhenguang Zhang and Andrew Loudon, date: 04/20/2020, view: 2909, 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 ...
    Assembly of Genetic Circuits with the Mammalian ToolKit
    Authors:  João P. Fonseca, Alain R Bonny, Jason Town and Hana El-Samad, date: 03/05/2020, view: 3915, Q&A: 0
    [Abstract] The ability to rapidly assemble and prototype cellular circuits is vital for biological research and its applications in biotechnology and medicine. The Mammalian ToolKit (MTK) is a Golden Gate-based cloning toolkit for fast, reproducible and versatile assembly of large DNA vectors and their implementation in mammalian models. The MTK consists of ...
    Approaching RNA-seq for Cell Line Identification
    Authors:  Tabrez A. Mohammad and Yidong Chen, date: 02/05/2020, view: 3052, Q&A: 0
    [Abstract] Cancer cell lines serve as invaluable model systems for cancer biology research and help in evaluating the efficacy of new therapeutic agents. However, cell line contamination and misidentification have become one of the most pressing problems affecting biomedical research. Available methods of cell line authentication suffer from limited access, ...
    Microarray, IPA and GSEA Analysis in Mice Models
    [Abstract] This protocol details a method to analyze two tissue samples at the transcriptomic level using microarray analysis, ingenuity pathway analysis (IPA) and gene set enrichment analysis (GSEA). Methods such as these provide insight into the mechanisms underlying biological differences across two samples and thus can be applied to interrogate a variety ...
    RNA Interference Screening to Identify Proliferation Determinants in Breast Cancer Cells
    [Abstract] RNAi screening technology has revealed unknown determinants of various biological signaling pathways in biomedical studies. This protocol provided detailed information about how to use RNAi screening to identify proliferation determinants in breast tumor cells. siRNA-based libraries targeting against Estrogen receptor (ER)-network, including 631 ...
    Synthetic Lethality Screens Using RNAi in Combination with CRISPR-based Knockout in Drosophila Cells
    Authors:  Benjamin E. Housden, Hilary E. Nicholson and Norbert Perrimon, date: 02/05/2017, view: 9751, Q&A: 0
    [Abstract] A synthetic lethal interaction is a type of genetic interaction where the disruption of either of two genes individually has little effect but their combined disruption is lethal. Knowledge of synthetic lethal interactions can allow for elucidation of network structure and identification of candidate drug targets for human diseases such as cancer. ...
    Lentiviral shRNA Screen to Identify Epithelial Integrity Regulating Genes in MCF10A 3D Culture
    Authors:  Elsa Marques and Juha Klefström, date: 12/05/2016, view: 9703, Q&A: 0
    [Abstract] MCF10A 3D culture system provides a reductionist model of glandular mammary epithelium which is widely used to study development of glandular architecture, the role of cell polarity and epithelial integrity in control of epithelial cell functions, and mechanisms of breast cancer. Here we describe how to use shRNA screening approach to identify ...

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