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丁香实验推荐阅读
Isolation of Intracellular Protein DNA Complexes Using HaloCHIP, an Antibody-Free Alternative to Chromatin Immunoprecipitation

Mapping of protein binding sites within the genome has been significantly advanced by microarray and sequencing technologies, yet the method traditionally used to isolate protein–DNA complexes, chromatin immunoprecipitation, has remained dependent of the use of antibodies. ...

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Application of mRNA Display for In Vitro Selection of DNA-Binding Transcription Factor Complexes

Comprehensive analysis of DNA–protein interactions is important for mapping transcriptional regulatory networks at the genome-wide level. Here, we present a new application of mRNA display, using the in vitro virus (IVV) technology, for in vitro selection of DNA-binding protein com ...

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Promoter Deletion Analysis Using a Dual-Luciferase Reporter System

Promoter deletion analysis is a useful tool for identifying important regulatory regions involved in transcriptional control of gene expression. In this approach, a series of promoter deletion fragments are fused to a reporter gene, such as chloramphenicol acetyltransferase or l ...

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Luciferase Assay to Study the Activity of a Cloned Promoter DNA Fragment

Luciferase based assays have become an invaluable tool for the analysis of cloned promoter DNA fragments, both for verifying the ability of a potential promoter fragment to drive the expression of a luciferase reporter gene in various cellular contexts, and for dissecting binding elemen ...

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Acquisition of High Quality DNA for Massive Parallel Sequencing by In Vivo Chromatin Immunoprecipitation

ChIP-seq is rapidly becoming a routine technique for the determination of the genome wide association of DNA binding proteins and histone modifications. Here we provide a protocol for the isolation, purification, and immunoprecipitation of DNA fragments associated with a target tra ...

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Practical Informatics Approaches to Microsatellite and Variable Number Tandem Repeat Analysis

The second most common source of genetic variation after SNPs is polymorphic tandem repeats, the alleles of which consist of a variable number of repeated units that can be either small (e.g., CA) or large (to 100 nucleotides in length). There are perhaps over half a million of these in the human genome. They h ...

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Assessing the Impact of Genetic Variation on Transcriptional Regulation In Vitro

Two alleles of a gene that contain polymorphic cis-regulatory regions can contribute differently to expression levels. Evolutionary changes in such cis-regulatory domains are believed to have participated in the cognitive evolution of H. sapiensas well as phenotypic diversity. ...

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Whole Genome Sequencing

Whole genome sequencing provides the most comprehensive collection of an individual’s genetic variation. With the falling costs of sequencing technology, we envision paradigm shift from microarray-based genotyping studies to whole genome sequencing. We review methodolog ...

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An Introduction to Mitochondrial Informatics

In this chapter, we review the public resources available for human mitochondrial DNA and protein related bioinformatics, with a special focus on mitochondrial single nucleotide polymorphisms (mtSNPs). We also review our own freeware tool V-MitoSNP, giving an overview of its impleme ...

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Detection of Mitochondrial DNA Variation in Human Cells

The ability to detect mitochondrial DNA (mtDNA) variation within human cells is important not only to identify mutations causing mtDNA disease, but also as mtDNA mutations are being increasingly described in many ageing tissues and in complex diseases such as diabetes, neurodegenera ...

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Web-Based Analysis of (Epi-) Genome Data Using EpiGRAPH and Galaxy

Modern life sciences are becoming increasingly data intensive, posing a significant challenge for most researchers and shifting the bottleneck of scientific discovery from data generation to data analysis. As a result, progress in genome research is increasingly impeded by bioin ...

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Asking Complex Questions of the Genome Without Programming

Increasingly, vast amounts of genomics and genetic data are available. Although much of the data is largely accessible to relatively simple web queries, in some cases, more complex queries are required. This paper reviews the hierarchy of tools for querying genetic and genomic data. For query ...

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Exploring the Landscape of the Genome

Genome browsers are powerful tools for biologists - offering fundamental information on genes, regulatory elements, genomic variants, genome structure, and evolution. The comprehensive range of information presented in tools such as the UCSC genome browser and Ensembl enables i ...

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Gaining a Pathway Insight into Genetic Association Data

The recent application of high throughput genotyping in humans has yielded numerous insights into the genetic basis of human phenotypes and unprecedented amount of genetic variation data. Each genome wide significant finding has explained only a tiny proportion of phenotypic vari ...

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Genetic Variation Analysis for Biomedical Researchers: A Primer

Biomedical researchers studying gene function should consider the impact of variation, even if genetics is not the primary objective of an investigation. Information on genetic variation can provide a valuable insight into the functional range and critical regions of a gene, protein or ...

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Analysis of the Impact of Genetic Variation on Human Gene Expression

Interindividual variation in gene expression has been convincingly shown to be controlled, in part, by genetic differences. Determining the architecture of genetic variation, the underlying gene expression may allow deeper insight into complex phenotypes, such as differences ...

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Bioinformatic Tools for Identifying Disease Gene and SNP Candidates

As databases of genome data continue to grow, our understanding of the functional elements of the genome grows as well. Many genetic changes in the genome have now been discovered and characterized, including both disease-causing mutations and neutral polymorphisms. In addition to expe ...

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Short Tandem Repeats and Genetic Variation

Single nucleotide polymorphisms (SNPs) are widely distributed in the human genome and although most SNPs are the result of independent point-mutations, there are exceptions. When studying distances between SNPs, a periodic pattern in the distance between pairs of identical SNPs has b ...

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Laboratory Methods for the Detection of Chromosomal Abnormalities

Constitutional chromosomal aberrations are inborn changes with or without phenotypic consequences. Conventional chromosome analysis has been for a long time the method of choice for identification of such abnormalities. However, over the past decades, several molecular cyto ...

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Cancer Genome Analysis Informatics

The analysis of cancer genomes has benefited from the advances in technology that enable data to be generated on an unprecedented scale, describing a tumour genome’s sequence and composition at increasingly high resolution and reducing cost. This progress is likely to increase further o ...

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