Integrating RNA-seq and Epigenomic Data Analysis

Inquiry

Gene expression is strongly regulated by DNA methylation and chromatin dynamics; binding sites associated with chromatin modifications are often integrated with transcriptomics data to discover genes regulated by specific proteins. Transcriptomics data can also be integrated with open chromatin regions to accurately assess gene regulation patterns. Methylation profiles can likewise be integrated with other epigenomic or transcriptomic measurements to understand the role of methylation on gene over- or under-expression.

Specific Integrating RNA-seq and Epigenomic Data Analysis Approaches We Offer

CD Genomics can perform comprehensive analysis of RNA-seq and apparent genome (such as ChIP or ATAC- seq) for the same book to study the genetic regulation procedures of the whole genome.
Based on the evidence of gene expression and regulatory components, CD Genomics can determine the regulatory connection between the enhancer and its target gene and transcription factor and its target.

What Type of Data Can We Combine?

ChIP-Seq with methylation
ATAC-Seq with methylation
mRNA-Seq with methylation data
sncRNA-Seq with ChIP-Seq or ATAC-Seq
mRNA-Seq with ChIP-Seq or ATAC-Seq

Complete analysis

Analysis

Comparative analysis aimed at finding differential responses between two groups of samples
Functional gene annotation on features with differential responses
Integration of two sets of omics data - linear regression
Gene ontology enrichment analysis of correlated features
Summary statistics for the different technologies used
Trimmed and filtered reads in fastQ files after sequencing QC
BAM sorted files from alignment to reference genome or transcriptome (indexed bam files and bigwig files included)

Results

List of peaks with their enrichment level (ChIP-Seq, ATAC-Seq, MeDIP-Seq)
List of CpGs with their methylation percentage (WGBS, RRBS, EPIC, BSAS)
Matrix with expression abundance estimation (total, messenger and small non-coding RNA)

Workflow

The central steps in the workflow include:

Workflow

Follow-up Experiments

Validating CRE-target interactions by chromosome conformation capture.
Validating the CRE-gene interactions with genome editing.
Validating TF-CRE interactions using ChIP-seq.

Service Process

Deliverables

Related experimental results raw data
Experimental report
Data analysis
Image and result analysis

Applications

DNA methylation.
Transcription factor binding and histone modifications.
Chromatin accessibility analysis
Chromatin conformational analysis

Our Features

We have accumulated many years of essence in the field of integrating RNA-seq and epigenomic data analysis service, helping customers to speed up project development and improve the overall success rate of the project.
At CD Genomics, simply let us know your specific project needs. We will suggest the best strategy for you.

Why Choose Us?

CD Genomics is a company that provides professional and comprehensive integrating RNA-seq and epigenomic data analysis service. We have years of experience to meet your specific project needs in using epigenomics research to add value to your research projects. CD Genomics can provide you with personalized solutions to help you thrive every step of the way around your interest in your workflow. If you would like to know more about this service, please feel free to contact us.

! For research purposes only, not intended for clinical diagnosis or individual assessments.