Showing papers in "Methods in 2009"
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TL;DR: How to perform ChIP-seq starting with whole tissues or cell lines, and ending with millions of short sequencing tags that can be aligned to the reference genome of the species under investigation is described.
494 citations
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TL;DR: The experimental approach for both sample preparation and data analysis for the technique of RNA-seq, which can generate quantitative expression scores that are comparable to microarrays, with the added benefit that the entire transcriptome is surveyed without the requirement of a priori knowledge of transcribed regions.
494 citations
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TL;DR: The molecular dynamics flexible fitting method for combining high-resolution atomic structures withcryo-electron microscopy maps, that results in atomic models representing the conformational state captured by cryo-EM, has been applied successfully to the ribosome.
315 citations
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TL;DR: The principles of the comet assay are reviewed and key studies that have focused on this assay in the past 25 years are cited and an example of how it was used in the authors' laboratory for studying the induction of DNA damage in human lung cancer cells after differing doses of the cytosine analog 5-aza-2'-deoxycytidine.
296 citations
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TL;DR: The use of the MSMBuilder package is described to build Markov State Models (MSMs) to identify the metastable states from Generalized Ensemble simulations, as well as other simulation datasets.
288 citations
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TL;DR: An extensive, optimized protocol for generating RRBS libraries is provided and the power of this strategy for methylome profiling is discussed, which includes information on sequence analysis and the relative coverage over genomic regions of interest for a representative mouse MspI generated RRBS library.
213 citations
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TL;DR: FAIRE has utility in establishing chromatin profiles of diverse cell types in health and disease, isolating DNA regulatory elements en masse for further characterization, and as a screening assay for the effects of small molecules on chromatin organization.
211 citations
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TL;DR: An overview of software that is appropriate for the analysis of high throughput sequencing data generated by Illumina/Solexa-type sequencing by synthesis, with a special emphasis on approaches and applications that can generate more accurate depictions of sequence reads that fall in repeated regions of a chosen reference genome.
206 citations
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TL;DR: This review summarizes the development of radiolabeled probes for peptide receptor imaging since the emergence of the technology with a particular focus on peptide radiopharmaceuticals developed during the last 5 years, and highlights the different factors which are decisive during the process of tracer development and evaluation.
195 citations
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TL;DR: This paper describes protocols for studies of structure and dynamics of DNA and protein-DNA complexes with atomic force microscopy (AFM) utilizing the surface chemistry approach, including the protocols for synthesis of silatranes.
175 citations
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TL;DR: The detailed protocol describes the creation of an integration standard cell line and accompanying standard curve, as well as the quantitation of integration and calculation of associated error estimates, and speculation on fundamental, unresolved issues in HIV latency that can be addressed by measuring HIV integration.
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TL;DR: The Random Forest regression method is presented as a way of accounting for interacting loci in order to detect (epistatic) interactions between distant genetic loci one has to take into account several loci simultaneously.
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TL;DR: A simple and practical system that couples a microfluidic platform with an array of micro-bioreactors, and has the size of a microscope slide is designed, which allows quantitative studies of cells cultured in monolayers or encapsulated in three-dimensional hydrogels.
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TL;DR: An overview is provided on contrast generation strategies for MRI of cells, which includes MR contrast agents, various approaches of cell labeling and MRI as well as MR spectroscopic methods used for cell tracking in vivo.
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TL;DR: A detailed protocol for performing smFRET using total internal reflection fluorescence microscopy, including RNA preparation, optical setup, separation of the dual color channels, sample immobilization and data acquisition and analysis is presented.
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TL;DR: A method for synchronization of the cell cycle in the bacterium Escherichia coli, which can be used in fully wild-type cells, at different growth rates, and may be applicable to other bacterial species with replication control by the stringent response.
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TL;DR: An overview of the radiopharmaceutical development and in vivo evaluation of apoptosis and necrosis detecting radioligands that have emerged so far is provided.
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TL;DR: This work provides two detailed protocols to apply SB-mediated, non-viral gene transfer in cultured cells and shows how to achieve 40-50% stable expression of a transgene in clinically relevant, hard-to-transfect cells (hematopoetic stem cells, HSCs) by nucleofection.
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TL;DR: The protocols to perform Gal4 gene trap and enhancer trap screens in zebrafish and their application to the studies of vertebrate neural circuits are described.
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TL;DR: UV cross-linking and immunoprecipitation assay (CLIP) can identify direct interaction sites between RNA-binding proteins and RNAs in vivo, and has been used to study several proteins in tissues and cell cultures.
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TL;DR: It is demonstrated that a composite scaffold can be fabricated with two completely different polymer systems for the engineering of hollow organs and are able to form tissues in vivo.
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TL;DR: Validation of the dataset using a machine learning approach trained to minimize the rate of false positives and false negatives yielded a high-confidence dataset and uncovered novel interactors that regulate the RNAPII transcription machinery, including a new protein assembly the authors named theRNAPII-Associated Protein 3 (RPAP3) complex.
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TL;DR: It is time to study performance of BN analogues for peptide receptor based imaging in patients validating results of PC imaging using histopathology as a golden standard.
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TL;DR: This review focuses on best practices for planning, designing and executing effective ITC experiments when one or more of the reactants is an RNA.
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TL;DR: Practical guidelines for the setup of MD simulations, the choice of ionic conditions and the detection and correction of experimental inaccuracies in order to start MD simulations of nucleic acid systems under the best auspices are provided.
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TL;DR: This review surveys methodology as well as recent advances in QM/MM applications to RNA mechanisms, including those of the HDV, hairpin, and hammerhead ribozymes, as wellAs the ribosome, to jointly advance understanding of RNA catalysis at an atomistic level.
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TL;DR: The unconventional collimation and the more stringent resolution requirements pose problems that are not present in clinical SPECT imaging that can be solved to implement micro-SPECT imaging on a rotating gamma camera.
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TL;DR: The observed formation of small tooth-like structures consisting of organized dentin, enamel, pulp, cementum, periodontal ligament, and surrounded by regenerated alveolar bone, suggests the feasibility for regeneration of teeth and associated alveolars bone, in a single procedure.
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TL;DR: Techniques for coupling ChIP-chip/ChIP-seq with genetic, chemical, and experimental manipulation are described to obtain mechanistic insight from genome-wide protein-DNA binding studies, and a critical role is inferred for the transition between initiation and full elongation competence is inferred.
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TL;DR: A culture technique is established for human MPCs that allows for reliable cell growth and expansion using collagen coated dishes and defined media only and demonstrated a muscle phenotype and the ability to form myofibers in vitro.