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ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest.
ChIP has also been applied for genome-wide analysis by combining with microarray technology (ChIP-on-chip) or second-generation DNA-sequencing technology (Chip-Sequencing). ChIP can also combine with paired-end tags sequencing in Chromatin Interaction Analysis using Paired End Tag sequencing (ChIA-PET), a technique developed for large-scale, de ...
Suite of tools for assembly, alignment, and analysis of short read next generation sequencing data Unix/Linux, macOS: GPL: BGI: Staden Package: Sequence assembly, editing, and analysis, mainly consisting of gap4, gap5, and spin. Written in C, C++, Fortran and Tcl. Linux, macOS, Windows: BSD: Wellcome Trust Sanger Institute, Medical Research Council
Wilbanks and colleagues [3] is a survey of the ChIP-seq peak callers, and Bailey et al. [4] is a description of practical guidelines for peak calling in ChIP-seq data. Peak calling may be conducted on transcriptome/exome as well to RNA epigenome sequencing data from MeRIPseq [ 5 ] or m6Aseq [ 6 ] for detection of post-transcriptional RNA ...
The ChIA-PET method combines ChIP-based methods, [2] and Chromosome conformation capture (3C) based methods, [3] to extend the capabilities of both approaches. ChIP-Sequencing (ChIP-Seq) is a popular method used to identify transciption factor binding sites (TFBS) while 3C has been used to identify long-range chromatin interactions.
Introduced in 2007, ChIP sequencing (ChIP-seq) is a technology that uses chromatin immunoprecipitation to crosslink the proteins of interest to the DNA but then instead of using a micro-array, it uses the more accurate, higher throughput method of sequencing to localize interaction points. [13]
The colour space data produced by the SOLiD platform can be decoded into DNA bases for further analysis, however software that considers the original colour space information can give more accurate results. Life Technologies has released BioScope, [26] a data analysis package for resequencing, ChiP-Seq and transcriptome analysis. It uses the ...
GenePattern is a freely available online platform that provides access to RNA-Seq analysis methods without the need for programming. GeneProf Freely accessible, easy to use analysis pipelines for RNA-seq and ChIP-seq experiments. GREIN is an interactive web platform for re-processing and re-analyzing GEO RNA-seq data. GREIN is powered by the ...