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Cell Type-specific Metabolic Labeling of Proteins with Azidonorleucine in Drosophila

Featured protocol,  Authors: Ines Erdmann
Ines ErdmannAffiliation 1: Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
Affiliation 2: Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg, Germany
Bio-protocol author page: a4841
Kathrin Marter
Kathrin MarterAffiliation 1: Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
Affiliation 2: Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg, Germany
Affiliation 3: Center for Behavioral Brain Sciences, Magdeburg, Germany
Bio-protocol author page: a4842
Oliver Kobler
Oliver KoblerAffiliation: Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany
Bio-protocol author page: a4843
Sven Niehues
Sven NiehuesAffiliation 1: Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany
Affiliation 2: Faculty of Medicine, University of Münster, Münster, Germany
Bio-protocol author page: a4844
Julia Bussmann
Julia BussmannAffiliation 1: Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany
Affiliation 2: Faculty of Medicine, University of Münster, Münster, Germany
Bio-protocol author page: a4845
Anke Müller
Anke MüllerAffiliation 1: Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
Affiliation 2: Research Group Neuralomics, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
Bio-protocol author page: a4846
Julia Abele
Julia AbeleAffiliation 1: Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
Affiliation 2: Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg, Germany
Bio-protocol author page: a4847
Erik Storkebaum
Erik StorkebaumAffiliation 1: Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany
Affiliation 2: Faculty of Medicine, University of Münster, Münster, Germany
Bio-protocol author page: a4848
Ulrich Thomas
Ulrich ThomasAffiliation: Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany
For correspondence: thomas@lin-magdeburg.de
Bio-protocol author page: a4849
 and Daniela C. Dieterich
Daniela C. DieterichAffiliation 1: Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
Affiliation 2: Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg, Germany
Affiliation 3: Center for Behavioral Brain Sciences, Magdeburg, Germany
For correspondence: daniela.dieterich@med.ovgu.de
Bio-protocol author page: a4850
date: 7/20/2017, 12 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2397.

Brief version appeared in Nat Commun, Jul 2015
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 tissue-embedded cells still poses a challenge, which we meet with a detailed version of our recently established protocol for cell-selective and temporally controllable metabolic labeling of proteins in Drosophila. This method is based on targeted expression of a mutated variant of methionyl-tRNA-synthetase, MetRSL262G, which allows for charging methionine tRNAs with the non-canonical amino acid azidonorleucine (ANL) and, thus, for detectable ANL incorporation into nascent polypeptide chains.

Cell Type-specific Metabolic Labeling of Proteins with Azidonorleucine in Drosophila

Authors: Ines Erdmann
Ines ErdmannAffiliation 1: Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
Affiliation 2: Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg, Germany
Bio-protocol author page: a4841
Kathrin Marter
Kathrin MarterAffiliation 1: Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
Affiliation 2: Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg, Germany
Affiliation 3: Center for Behavioral Brain Sciences, Magdeburg, Germany
Bio-protocol author page: a4842
Oliver Kobler
Oliver KoblerAffiliation: Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany
Bio-protocol author page: a4843
Sven Niehues
Sven NiehuesAffiliation 1: Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany
Affiliation 2: Faculty of Medicine, University of Münster, Münster, Germany
Bio-protocol author page: a4844
Julia Bussmann
Julia BussmannAffiliation 1: Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany
Affiliation 2: Faculty of Medicine, University of Münster, Münster, Germany
Bio-protocol author page: a4845
Anke Müller
Anke MüllerAffiliation 1: Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
Affiliation 2: Research Group Neuralomics, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
Bio-protocol author page: a4846
Julia Abele
Julia AbeleAffiliation 1: Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
Affiliation 2: Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg, Germany
Bio-protocol author page: a4847
Erik Storkebaum
Erik StorkebaumAffiliation 1: Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany
Affiliation 2: Faculty of Medicine, University of Münster, Münster, Germany
Bio-protocol author page: a4848
Ulrich Thomas
Ulrich ThomasAffiliation: Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany
For correspondence: thomas@lin-magdeburg.de
Bio-protocol author page: a4849
 and Daniela C. Dieterich
Daniela C. DieterichAffiliation 1: Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
Affiliation 2: Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg, Germany
Affiliation 3: Center for Behavioral Brain Sciences, Magdeburg, Germany
For correspondence: daniela.dieterich@med.ovgu.de
Bio-protocol author page: a4850
date: 7/20/2017, 12 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2397.

[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 tissue-embedded ...

Validating Candidate Congenital Heart Disease Genes in Drosophila

Authors: Jun-yi Zhu*
Jun-yi ZhuAffiliation: Center for Cancer and Immunology Research, Children’s National Medical Center, 111 Michigan Ave. NW, Washington, DC, USA
Bio-protocol author page: a4710
Yulong Fu*
Yulong FuAffiliation: Center for Cancer and Immunology Research, Children’s National Medical Center, 111 Michigan Ave. NW, Washington, DC, USA
Bio-protocol author page: a4711
Adam Richman
Adam RichmanAffiliation: Center for Cancer and Immunology Research, Children’s National Medical Center, 111 Michigan Ave. NW, Washington, DC, USA
Bio-protocol author page: a4712
 and Zhe Han
Zhe HanAffiliation 1: Center for Cancer and Immunology Research, Children’s National Medical Center, 111 Michigan Ave. NW, Washington, DC, USA
Affiliation 2: Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
For correspondence: zhan@childrensnational.org
Bio-protocol author page: a4713
 (*contributed equally to this work) date: 6/20/2017, 227 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2350.

[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 disease (CHD) genes. The protocols ...

A Method to Convert mRNA into a Guide RNA (gRNA) Library without Requiring Previous Bioinformatics Knowledge of the Organism

Author: Hiroshi Arakawa
Hiroshi ArakawaAffiliation: IFOM–FIRC Institute of Molecular Oncology Foundation, Milan, Italy
For correspondence: hiroshi.arakawa@ifom.eu
Bio-protocol author page: a4565
date: 5/20/2017, 418 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2319.

[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 ...

Next-generation Sequencing of the DNA Virome from Fecal Samples

Authors: Cynthia L. Monaco
Cynthia L. MonacoAffiliation: Department of Medicine, Washington University School of Medicine, St. Louis, USA
For correspondence: cmonaco@wustl.edu
Bio-protocol author page: a4038
 and Douglas S. Kwon
Douglas S. KwonAffiliation 1: Ragon Institute of MGH, MIT, and Harvard, Cambridge, USA
Affiliation 2: Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, USA
Bio-protocol author page: a4039
date: 3/5/2017, 953 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2159.

[Abstract] Herein we describe a detailed protocol for DNA virome analysis of low input human stool samples (Monaco et al., 2016). This protocol is divided into four main steps: 1) stool samples are pulverized to evenly distribute microbial matter; 2) stool is enriched for virus-like particles and DNA is extracted by phenol-chloroform; 3) purified DNA is multiple-strand ...

Bioinformatic Analysis for Profiling Drug-induced Chromatin Modification Landscapes in Mouse Brain Using ChlP-seq Data

Authors: Yong-Hwee Eddie Loh
Yong-Hwee Eddie LohAffiliation: Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
Bio-protocol author page: a4094
Jian Feng
Jian FengAffiliation: Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
Bio-protocol author page: a4095
Eric Nestler
Eric Nestler Affiliation: Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
Bio-protocol author page: a4096
 and Li Shen
Li ShenAffiliation: Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
For correspondence: li.shen@mssm.edu
Bio-protocol author page: a4097
date: 2/5/2017, 1016 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2123.

[Abstract] Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a powerful technology to profile genome-wide chromatin modification patterns and is increasingly being used to study the molecular mechanisms of brain diseases such as drug addiction. This protocol discusses the typical procedures involved in ChIP-seq data generation, ...

Protocol for Molecular Dynamics Simulations of Proteins

Authors: MNV Prasad Gajula
MNV Prasad GajulaAffiliation 1: Institute of Biotechnology, PJTSAU, Rajendra Nagar, Hyderabad, India
Affiliation 2: Bioclues.org, Kukatpally, Telangana, India
For correspondence: gajula.ibt@gmail.com
Bio-protocol author page: a3836
Anuj Kumar
Anuj KumarAffiliation: Bioinformatics center, Uttarakhand Council for Biotechnology,, Dehradun, India
Bio-protocol author page: a3837
 and Johny Ijaq
Johny IjaqAffiliation: Department of Zoology, Osmania University, Hyderabad, India
Bio-protocol author page: a3838
date: 12/5/2016, 2219 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2051.

[Abstract] Molecular dynamics (MD) simulations have become one of the most important tools in understanding the behavior of bio-molecules on nanosecond to microsecond time scales. In this protocol, we provide a general approach and standard setup protocol for MD simulations by using the Gromacs MD suite. ...

Sequencing of Ebola Virus Genomes Using Nanopore Technology

Author: Thomas Hoenen
Thomas HoenenAffiliation: Friedrich-Loeffler-Institut, Greifswald – Isle of Riems, Germany
For correspondence: thomas.hoenen@fli.de
Bio-protocol author page: a3685
date: 11/5/2016, 1309 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1998.

[Abstract] Sequencing of virus genomes during disease outbreaks can provide valuable information for diagnostics, epidemiology, and evaluation of potential countermeasures. However, particularly in remote areas logistical and technical challenges can be significant. Nanopore sequencing provides an alternative to classical Sanger and next-generation sequencing ...

Metabolite Profiling of Mature Arabidopsis thaliana Seeds Using Gas Chromatography-Mass Spectrometry (GC-MS)

Authors: Hagai Cohen
Hagai CohenAffiliation 1: Laboratory of Plant Science, Migal Galilee Technology Center, Kiryat Shmona, Israel
Affiliation 2: Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
For correspondence: Hagaic@Weizmann.ac.il
Bio-protocol author page: a3644
Ifat Matityahu
Ifat MatityahuAffiliation: Laboratory of Plant Science, Migal Galilee Technology Center, Kiryat Shmona, Israel
Bio-protocol author page: a3645
 and Rachel Amir
Rachel AmirAffiliation 1: Laboratory of Plant Science, Migal Galilee Technology Center, Kiryat Shmona, Israel
Affiliation 2: Tel-Hai College, Upper Galilee, Israel
For correspondence: Rachel@migal.org.il
Bio-protocol author page: a3646
date: 11/5/2016, 1320 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1981.

[Abstract] Metabolite profiling using gas chromatography-mass spectrometry (GC-MS) permits the annotation and quantification of a relatively wide variety of metabolites, covering a wide range of biochemical groups of metabolites. Lisec et al. (2006) established a method for GC-MS profiling in plants. Based on this protocol, we provide here a detailed GC-MS-based ...

Chromosome Dosage Analysis in Plants Using Whole Genome Sequencing

Authors: Ek Han Tan
Ek Han TanAffiliation: Plant Biology Dept. and Genome Center, University of California, Davis, USA
Bio-protocol author page: a3267
Luca Comai
Luca ComaiAffiliation: Plant Biology Dept. and Genome Center, University of California, Davis, USA
Bio-protocol author page: a3268
 and Isabelle M. Henry
Isabelle M. HenryAffiliation: Plant Biology Dept. and Genome Center, University of California, Davis, USA
For correspondence: imhenry@ucdavis.edu
Bio-protocol author page: a3269
date: 7/5/2016, 1984 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1854.

[Abstract] Relative chromosome dosage, i.e., increases or decreases in the number of copies of specific chromosome regions in one sample versus another, can be determined using aligned read-counts from Illumina sequencing (Henry et al., 2010). The following protocol was used to identify the different classes of aneuploids that result from uniparental genome elimination ...

Computational Identification of MicroRNA-targeted Nucleotide-Binding Site-Leucine-Rich Repeat Genes in Plants

Authors: Zhu-Qing Shao*
Zhu-Qing ShaoAffiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
Bio-protocol author page: a2675
Yan-Mei Zhang*
Yan-Mei ZhangAffiliation 1: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
Affiliation 2: Institute of Botany, Jiangsu Province & Chinese Academy of Science, Nanjing, China
Bio-protocol author page: a2676
Bin Wang
Bin WangAffiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
For correspondence: binwang@nju.edu.cn
Bio-protocol author page: a2677
 and Jian-Qun Chen
Jian-Qun ChenAffiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
For correspondence: chenjq@nju.edu.cn
Bio-protocol author page: a2678
 (*contributed equally to this work) date: 11/5/2015, 2224 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1637.

[Abstract] Plant genomes harbor dozens to hundreds of nucleotide-binding site-leucine-rich repeat (NBS-LRR, NBS for short) type disease resistance genes (Shao et al., 2014; Zhang et al., 2015). Proper regulation of these genes is important for normal growth of plants by reducing unnecessary fitness costs in the absence of pathogen infection. Recent studies have ...
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Nuclear Extraction from Arabidopsis thaliana

Authors: Fang Xu
Fang XuAffiliation: Department of Botany and Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
For correspondence: xufang@mail.ubc.ca
Bio-protocol author page: a188
 and Charles Copeland
Charles CopelandAffiliation: Department of Botany and Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
Bio-protocol author page: a189
date: 12/20/2012, 11771 views, 6 Q&A
DOI: https://doi.org/10.21769/BioProtoc.306.

[Abstract] This protocol is to isolate nuclei from Arabidopsis cells. They can be further used for other experiments, such as nuclear protein detection, nuclear protein immunoprecipitation and so on....

Illumina Sequencing Library Construction from ChIP DNA

Author: Wei Zheng
Wei ZhengAffiliation: Keck Biotech Services, Yale University, New Haven, USA
For correspondence: wei.zheng.madison@gmail.com
Bio-protocol author page: a10
date: 2/20/2012, 10740 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.91.

[Abstract] The Illumina sequencing platform is very popular among next-generation sequencing platforms. However, the DNA sequencing library construction kit provided by Illumina is considerably expensive. The protocol described here can be used to construct high-quality sequencing libraries from chromatin immunoprecipitated ...

[Bio101] Protein-ligand Binding Assay by Liquid Chromatography-Mass Spectrometry

Author: Xiyan Li
Xiyan LiAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: lixiyan@stanford.edu
Bio-protocol author page: a13
date: 8/20/2011, 10035 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.124.

[Abstract] Protein-small molecule binding coefficients are determined by quantitative LC-MS in this method. Traditional biochemical plot is consequently used to set up the binding curve between a known protein and a small molecule (<1000 Da) to determine the affinity constant (Kd) and the stoichiometry (Bmax)....

Quantitative Methylation Specific PCR (qMSP)

Authors: Triantafillos Liloglou
Triantafillos LiloglouAffiliation: Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
For correspondence: tliloglo@liv.ac.uk
Bio-protocol author page: a778
 and Georgios Nikolaidis
Georgios NikolaidisAffiliation: Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
Bio-protocol author page: a779
date: 8/20/2013, 9770 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.871.

[Abstract] Detection of low copies of methylated DNA targets in clinical specimens is challenging. The quantitative Methylation-Specific PCR (qMSP) assays were designed to specifically amplify bisulphite-converted methylated DNA target sequences in the presence of an excess of unmethylated counterpart sequences. ...

[Bio101] Affinity Purification of Yeast Protein-interacting Metabolites for ESI-MS Analysis

Author: Xiyan Li
Xiyan LiAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: lixiyan@stanford.edu
Bio-protocol author page: a13
date: 4/20/2011, 9497 views, 5 Q&A
DOI: https://doi.org/10.21769/BioProtoc.61.

[Abstract] The method described here can be used to discover in vivo protein-metabolite interactions. Metabolite-protein complexes are purified from yeast cell lysates by an affinity tag that recognizes the protein of interest. The protein-bound metabolites are extracted for identification by mass spectrometry, ...

[Bio101] Rabbit IgG Conjugation to Dynabeads

Author: Xiyan Li
Xiyan LiAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: lixiyan@stanford.edu
Bio-protocol author page: a13
date: 5/5/2011, 9461 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.63.

[Abstract] This method couples rabbit IgG (or any other proteins serve as affinity reagent) to the surface of magnetic beads (Brand name: Dynabeads). The amine and thiol groups of amino acid residues on the protein are covalently linked with the epoxy group on Dynabeads. The coupled IgG beads can be stored at ...

[Bio101] In-Solution Digestion Of Purified Yeast Protein For LC-MS

Author: Xiyan Li
Xiyan LiAffiliation: Department of Genetics, Stanford University, Stanford , USA
For correspondence: lixiyan@stanford.edu
Bio-protocol author page: a13
date: 4/20/2011, 8372 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.62.

[Abstract] This method describes the preparation of total yeast protein extract for mass spectrometry analysis. The protein extract is digested by trypsin in a solution with strong denaturants. The digested sample is dried and re-constituted in a mixture compatible with HPLC separation. Samples of isobaric labels ...

Construction and Screening of a Transposon Insertion Library of Yersinia enterocolitica (YeO3-R1)

Authors: Maria Pajunen
Maria PajunenAffiliation: Department of Biosciences, Division of Biochemistry and Biotechnology, University of Helsinki, Helsinki, Finland
Bio-protocol author page: a79
Elise Pinta
Elise PintaAffiliation: Department of Medical Biochemistry and Genetics, University of Turku, Turku, Finland
Bio-protocol author page: a80
 and Mikael Skurnik
Mikael SkurnikAffiliation: Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki, Helsinki, Finland
For correspondence: mikael.skurnik@helsinki.fi
Bio-protocol author page: a78
date: 8/5/2012, 6640 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.246.

[Abstract] The Mu-transposon system is one of the best characterized transposition systems. Under minimal in vitro set-up, Mu transposition requires only a simple reaction buffer, MuA transposase protein, mini-Mu transposon DNA (donor) and target DNA. The reaction proceeds via initial assembly of the transposition ...

Gene Networks Based on the Graphical Gaussian Model

Author: Shisong Ma
Shisong MaAffiliation: Department of Plant Biology & Genome Center, University of California, Davis, USA
For correspondence: sma@ucdavis.edu
Bio-protocol author page: a23
date: 2/20/2012, 6630 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.119.

[Abstract] This protocol describes how to build a gene network based on the graphical Gaussian model (GGM) from large scale microarray data. GGM uses partial correlation coefficient (pcor) to infer co-expression relationship between genes. Compared to the traditional Pearson’ correlation coefficient, partial correlation ...

Probing Yeast Protein Microarrays for Protein-protein Interactions Using V5-epitope Tagged Fusion Protein Probes

Authors: Joseph Fasolo
Joseph FasoloAffiliation: Department of Genetics, Stanford University, Stanford, USA
Bio-protocol author page: a22
 and Michael Snyder
Michael SnyderAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: mpsnyder@stanford.edu
Bio-protocol author page: a1789
date: 3/5/2012, 6537 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.123.

[Abstract] Protein microarray is probably the only technique currently available for systematic investigation of protein-protein interactions. This protocol describes an optimized method to probe yeast protein microarrays for protein-protein interactions using purified V5-epitope tagged fusion protein. It should ...
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