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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.
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 ...
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 packages for sequencing, searching, etc. written in C: Linux, macOS, Unix, Windows [4] GPL and LGPL: Collaborative project Galaxy: Scientific workflow and data integration system Unix-like: Academic Free: Collaborative project GenePattern: Scientific workflow system that provides access to hundreds of genomic analysis tools
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.
Cross-linking and immunoprecipitation (CLIP, or CLIP-seq) is a method used in molecular biology that combines UV crosslinking with immunoprecipitation in order to identify RNA binding sites of proteins on a transcriptome-wide scale, thereby increasing our understanding of post-transcriptional regulatory networks.
CLIP has first been combined with high throughput sequencing in HITS-CLIP to determine Nova-RNA binding sites in the mouse brain, [12] and in iCLIP that enabled amplification of truncated cDNAs and introduced the use of UMIs. [13] ChIP-on-chip: A similar technique which detects the binding of proteins to genomic DNA rather than RNA. [14]
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 ...