Validation by qPCR on a positive and a negative control region
Library preparation on ChIP sample and input
Sequencing (average of 30-50M raw reads, SE50 on Illumina HiSeq3000/4000)
Bioinformatic analysis including:
QC of raw reads with trimming and filtering if necessary
Filtering of black-listed regions
Alignment of quality filtered reads to reference genome
Removal of multimapping reads and PCR duplicates to provide uniquely aligned reads
Peak calling that identifies the regions with enrichment in the IP sample normalized to the input
Chromatin consists of DNA, histones and non-histone proteins. In forming chromatin, DNA is tightly wrapped around histones. Generally, more highly condensed chromatin is less accessible to transcription factors and other DNA binding proteins to access DNA, which has consequences for gene expression. Understanding the roles of histones and transcription factors is critical in understanding the regulation of gene expression.
Using ChIP-seq analysis, it is possible to profile histone modifications and transcription factor binding genome-wide to understand the regulation of gene expression in disease or in response to a drug treatment. Diagenode’s Epigenomic Profiling Services offer a wide variety of chromatin analysis options through ChIP-seq and ATAC-seq.
Post-translational modification of histones is implicated in the regulation of gene expression, necessitating the study of regulatory elements and their interacting proteins like active promoter and enhancer analysis. Profile genome-wide histone modifications by ChIP-seq analysis to understand transcriptional regulation
Active promoter profiling: H3K4me3 enrichment
Inactive promoter profiling: H3K27me3 enrichment
Enhancer profiling: H3K4me1 and H3K27ac enrichment in regulatory regions