Epigenome

Chromatin immunoprecipitation of a DNA-binding protein, coupled with next-generation sequencing (ChIP-seq), is one of the most widely used methods for measuring high-throughput epigenomics. From these data, we can identify protein binding sites across the genome. We provide a list of significant peaks that are annotated with the genomic position and statistical information, such as duration, number of reads, meaning p-values, location relative to the nearest genes (distance to TSS), location within genes (exon, intron, UTR), and the binding motif contained within peak. The binding sites are often analyzed in tandem with transcriptomics data in order to identify the genes that the DNA-binding protein is likely to be of interest under control. If there are data on expression, expression of the nearest gene will also be included to promote the correlation.

Deliverables:

· Statistically significant binding locations

· Functional annotation of the binding loci

· Comparison of binding events between samples

Pulling down and sequencing the DNA results in genome-wide epigenomics data indicating the positions of modified histones by using antibodies that target specific histone modifications. Targeting multiple different markers and integrating the data can reveal a map of chromatin state indicating promoters, active and inactive enhancers and actively transcribed genes. Besides the completely annotated histone positions with different modifications, we can also provide an explanation of the chromatin state, given sufficient measurements of various modifications.

Deliverables:

· Statistically significant binding locations with functional annotation

· Comparison of binding events between samples

· Chromatin state interpretation based on combinations of histone modifications

Adding methyl groups to cytosines in DNA shifts nearby gene expression rates. You can either pull down and sequence methylated DNA (MeDIP-seq) or convert unmethylated cytosines to uracil and sequenced (bisulphite sequencing). We will map, annotate and compare the methylated CpG islands using a variety of protocols to make analysis of your findings simpler for you. Methylation profiles can also be integratively analyzed using other epigenomics or transcriptomics measurements.

Deliverables:

· Quantification of methylation for all CpG islands

· Functional annotation for differentially methylated CpG islands

· Methylated individual cytosines (for BS- and RRBS-seq) 

Chromatin's complex state is a central focus of epigenomics, and can be analyzed throughout the genome by testing the chromatin's openness. Genome segments that aren't densely packed can be traced using ATAC sequencing. Open chromatin is linked to active regions in terms of gene expression or expression regulation. Transcriptomics data are therefore normally integrated with open chromatin information. Our analysis will indicate regions of open chromatin, with annotations about what genes are within that region and how the regions between your samples may have changed.

Deliverables:

· Loci of open chromatin

· Differentially open chromatin between samples

· Functional annotation of open chromatin loci