Table of Contents
Is ChIP-seq high-throughput?
Background. The combination of chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) has become the method of choice for mapping chromatin-associated proteins and histone-modifications on a genome-wide level. The ChIP-seq methodology has rapidly developed [1,2,3,4].
What is GVIZ?
The Gviz package aims to provide a structured visualization framework to plot any type of data along genomic coordinates. It also allows to integrate publicly available genomic annotation data from sources like UCSC or ENSEMBL.
What does a ChIP assay tell you?
Typically, ChIP is used to identify the relative abundance of a specific protein or a specific protein modification at a certain region in the genome. ChIP can be used to answer a multitude of scientific questions involving the interaction of proteins and chromatin.
Where do I find ChIP-seq data?
To see which ChIP-seq data sets are available for the Grhl proteins, go to http://cistrome.org/db/#/, type “Grhl” in the search box and click on Search. We can then refine the search further by selecting Homo sapiens under Species.
What does ATAC-seq measure?
What is ATAC-Seq? The assay for transposase-accessible chromatin with sequencing (ATAC-Seq) is a popular method for determining chromatin accessibility across the genome. By sequencing regions of open chromatin, ATAC-Seq can help you uncover how chromatin packaging and other factors affect gene expression.
What is a TxDb object?
Description. The TxDb class is a container for storing transcript annotations.
What do ChIP-seq peaks mean?
With ChIP-seq, the alignment of the reads to the genome results in two peaks (one on each strand) that flank the binding location of the protein or nucleosome of interest.
How do you validate ChIP-Seq data?
However, ChIP-qPCR is still the standard method to validate ChIP-Seq targets. Definitey it overcomes the biases of the Illumina sequencing (in case you get consistent results). You can always do knockdowns or knockouts, and see if the signal is disappearing from the target, or you can do positve and negative controls.
How do I work with ChIP-seq data in R/Bioconductor 28?
Working with ChIP-Seq Data in R/Bioconductor 28 can be supplied with a data frame of sample IDs and associated additional metadata. The rst column for addMetadata data frame must be SampleID and remaining columns may be categorical or discrete data.
How can I analyze ChIP-seq data?
Over the last years, an array of R/Bioconductor tools has been developed allowing researchers to process and analyze ChIP-seq data. This chapter provides an overview of the methods available to analyze ChIP-seq data based primarily on software packages from the open-source Bioconductor project.
How to get peaks from ChIP-seq in R?
ChIP-seq peak calling can also be done in R with the BayesPeak package. However, we stick here to the most common approach and use MACS. We ran MACS for you and provide the result in the data package. You can find the code necessary to obtain the peaks in the Appendix of the vignette.
How do I use ChIP-seq data for lysine 27 acetylation?
To exemplify this tutorial, we use ChIP-seq data for the lysine 27 acetylation of the histone H3 (i.e H3K27ac). 1. Read a ChIP-seq experiment into R 2. Extend the reads and bin the data (details and relevance discussed later) 3. Generate .bedGraph files 4. Visualize ChIP-seq data with R 5. Perform basic analysis of ChIP-seq peaks 6.