What is DNase seq used for?

DNase-seq (DNase I hypersensitive sites sequencing) is a method in molecular biology used to identify the location of regulatory regions, based on the genome-wide sequencing of regions sensitive to cleavage by DNase I.

What is the difference between ChIP-seq and RNA Seq?

ChIP-seq is run to map the global binding sites of the studied transcription factor, and RNA-seq is measured from the wild type and knockout model to identify genes regulated by the TF.

What is a ChIP-seq experiment?

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.

What is a ChIP-seq library?

ChIP-Seq identifies the binding sites of DNA-associated proteins and can be used to map global binding sites for a given protein. ChIP-Seq typically starts with crosslinking of DNA-protein complexes. Samples are then fragmented and treated with an exonuclease to trim unbound oligonucleotides.

What is CTCF binding site?

CTCF binds together strands of DNA, thus forming chromatin loops, and anchors DNA to cellular structures like the nuclear lamina. It also defines the boundaries between active and heterochromatic DNA. CTCF binding has also been both shown to promote and repress gene expression.

Why do researchers combine the techniques of RNA-Seq and ChIP-seq when trying to identify key transcription factor genes expressed in a tissue?

Combining ChIP-seq and RNA-seq assays can show agreement between both findings, revealing more information about a TF by either discovering a new function or a new set of genes for the same function [40].

Why is ChIP used?

Chromatin immunoprecipitation, or ChIP, is an antibody-based technology used to selectively enrich specific DNA-binding proteins along with their DNA targets. ChIP is used to investigate a particular protein-DNA interaction, several protein-DNA interactions, or interactions across the whole genome or a subset of genes.

What is ChIP assay used for?

The ChIP assay has become a very popular tool for studying chromatin structure and nuclear events involved in transcription. It has been used to identify target genes of many important DNA-binding proteins and their regulatory enzymes.

Is ChIP-seq expensive?

For high-resolution profiling of an entire large genome, ChIP-Seq is already less expensive than ChIP-chip; but depending on the genome size and the depth of sequencing needed, a ChIP-chip experiment on carefully selected regions using a customized microarray may yield as much biological understanding.

What is 4C sequencing?

4C-seq is a derivative 3C method, designed to search the genome for sequences contacting a selected genomic site of interest. 4C-seq employs inverse PCR and next generation sequencing to amplify, identify and quantify its proximity ligated DNA fragments.