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    Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq
    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 ...
    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 ...
    Extraction of DNA from Murine Fecal Pellets for Downstream Phylogenetic Microbiota Analysis by Next-generation Sequencing
    Authors:  Elien Eeckhout and Andy Wullaert, date: 02/05/2018, view: 98, Q&A: 0
    [Abstract] Mouse models are widely used to evaluate the potential impact of the gut microbial composition on health and disease. Standardized protocols for sampling and storing murine feces, as well as for extracting DNA from these fecal pellets are needed to limit experimental variation between different studies. Both efficient lysis of the microbiota and ...
    Extraction and Analysis of Pan-metabolome Polar Metabolites by Ultra Performance Liquid Chromatography–Tandem Mass Spectrometry (UPLC-MS/MS)
    Authors:  Dania M. Malik, Seth Rhoades and Aalim Weljie, date: 02/05/2018, view: 95, Q&A: 0
    [Abstract] Modern triple quadrupole mass spectrometers provide the ability to detect and quantify a large number of metabolites using tandem mass spectrometry (MS/MS). Liquid chromatography (LC) is advantageous, as it does not require derivatization procedures and a large diversity in physiochemical characteristics of analytes can be accommodated through a ...
    Identification and Quantification of Secondary Metabolites by LC-MS from Plant-associated Pseudomonas aurantiaca and Pseudomonas chlororaphis
    Authors:  Izzah Shahid, Muhammad Rizwan and Samina Mehnaz, date: 01/20/2018, view: 245, Q&A: 0
    [Abstract] Increased antibiotic resistance of plants and human pathogens and continuous use of chemical fertilizers has pushed microbiologists to explore new microbial sources as potential antagonists. In this study, eight strains of Pseudomonas aurantiaca and Pseudomonas chlororaphis, have been isolated from different plant sources and ...
    Brief Protocol for EDGE Bioinformatics: Analyzing Microbial and Metagenomic NGS Data
    [Abstract] Next-generation sequencing (NGS) offers unparalleled resolution for untargeted organism detection and characterization. However, the majority of NGS analysis programs require users to be proficient in programming and command-line interfaces. EDGE bioinformatics was developed to offer scientists with little to no bioinformatics expertise a ...
    Low-input Capture-C: A Chromosome Conformation Capture Assay to Analyze Chromatin Architecture in Small Numbers of Cells
    Authors:  A. Marieke Oudelaar, Damien J. Downes, James O.J. Davies and Jim R. Hughes, date: 12/05/2017, view: 1166, Q&A: 0
    [Abstract] Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This protocol describes two new low-input Capture-C approaches that can generate high-quality 3C interaction profiles from 10,000-20,000 cells, depending on the ...
    Lipidomic Analysis of Caenorhabditis elegans Embryos
    Authors:  Hung-Chi Yang, Cheng-Yu Hung, Yi-Yun Pan, Szecheng J Lo and Daniel Tsun-Yee Chiu, date: 09/20/2017, view: 1175, Q&A: 0
    [Abstract] Metabolomic is an emerging field of system biology. Lipidomic, a branch of metabolomic, aims to characterize lipophilic metabolites in biological systems. Caenorhabditis elegans (C. elegans) is a genetically tractable and versatile animal model for novel discovery of lipid metabolism. In addition, C. elegans embryo is ...
    Cell Type-specific Metabolic Labeling of Proteins with Azidonorleucine in Drosophila
    [Abstract] Advanced mass spectrometry technology has pushed proteomic analyses to the forefront of biological and biomedical research. Limitations of proteomic approaches now often remain with sample preparations rather than with the sensitivity of protein detection. However, deciphering proteomes and their context-dependent dynamics in subgroups of ...
    Validating Candidate Congenital Heart Disease Genes in Drosophila
    Authors:  Jun-yi Zhu, Yulong Fu, Adam Richman and Zhe Han, date: 06/20/2017, view: 1491, Q&A: 0
    [Abstract] Genomic sequencing efforts can implicate large numbers of genes and de novo mutations as potential disease risk factors. A high throughput in vivo model system to validate candidate gene association with pathology is therefore useful. We present such a system employing Drosophila to validate candidate congenital heart ...
    A Method to Convert mRNA into a Guide RNA (gRNA) Library without Requiring Previous Bioinformatics Knowledge of the Organism
    Author:  Hiroshi Arakawa, date: 05/20/2017, view: 2001, Q&A: 0
    [Abstract] While the diversity of species represents a diversity of special biological abilities, many of the genes that encode those special abilities in a variety of species are untouched, leaving an untapped gold mine of genetic information; however, despite current advances in genome bioinformatics, annotation of that genetic information is incomplete in ...