As one of the providers of oxidative bisulfite sequencing (oxBS-seq) analysis, CD Genomics uses bioinformatics to help you process Illumina short-read sequencing data from genome-wide oxBS-seq designed to unravel the function and interactions of the mammalian cytosine modifications 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). We provide convenient and fast biological data analysis services for scientific researchers all over the world.
Introduction to Oxidative Bisulfite Sequencing (oxBS-Seq) Analysis
DNA methylation is an epigenetic modification that affects genome organization and function and plays a critical role in both normal development and disease. 5mC and 5hmC are known DNA methylators involved in transcriptional repression, active demethylation and gene regulation, etc. Understanding the functional role of DNA methylation requires knowledge of its distribution in the genome. Bisulfite sequencing (BS-seq) has been the gold standard technique for studying DNA methylation at single-base resolution. However, BS-seq has limitations in distinguishing between 5mC and 5hmC. To overcome this limitation, oxBS-seq was developed, which for the first time quantitatively sequenced 5hmC at single-base resolution and was able to accurately locate 5hmC and 5mC. OxBS-seq data grew exponentially, but computational methods designed for oxBS-seq-specific problems were far inferior to other sequencing applications.
Fig. 1. Workflow of oxBS-seq. (Booth MJ, et al, 2013)
Application Field
Our oxBS-seq analysis can be used for but not limited to the following research:
Epigenetics: our oxBS-seq analysis enables the study of the interactions between DNA methylation and hydroxymethylation in different biological environments. It provides a comprehensive understanding of epigenetic modifications associated with gene regulation, cell differentiation and developmental processes.
Disease studies: by studying DNA methylation and hydroxymethylation patterns in disease samples, our oxBS-seq analysis can reveal epigenetic alterations associated with diseases such as cancer, neurological disorders, and cardiovascular disease.
Environmental epigenomics: our oxBS-seq analysis is widely used to study the effects of environmental factors on DNA methylation and hydroxymethylation. By comparing samples exposed to different environmental conditions, our researchers can help you identify epigenetic changes associated with environmental exposures and understand their potential impact on health and disease susceptibility.
Developmental biology: our oxBS-seq analysis can help you analyze the kinetics of DNA methylation during embryonic development and tissue differentiation, providing a high-resolution methylation profile.
CD Genomics Data Analysis Pipeline:
CD Genomics offers comprehensive services for oxidative bisulfite sequencing (oxBS-seq) bioinformatics analysis. Our team of highly skilled bioinformaticians utilize state-of-the-art tools and methods to process and interpret oxBS-seq data, providing valuable insights into DNA methylation and hydroxymethylation patterns.
(1) Data pre-processing
In the initial stage, we subject the raw sequencing data obtained from oxBS-seq experiments to thorough preprocessing steps. These steps involve adapter trimming, quality filtering and removal of low quality reads to ensure high quality data for downstream analysis.
(2) Genome alignment
Based on a specialized alignment algorithm for bisulfite conversion, we align the pre-processed oxBS-seq reads to the reference genome. This step allows the modified cytosines to be accurately mapped to their genomic positions.
(3) Cytosine methylation calling
CD Genomics uses state-of-the-art algorithms to call the methylation status of individual cytosines. These algorithms take advantage of the unique properties of oxBS-seq data and statistical models to accurately determine cytosine methylation levels.
(4) Differential methylation analysis
CD Genomics specializes in differential methylation analysis to identify significant changes in DNA methylation patterns between conditions or sample groups.
(5) Functional annotation and interpretation
To gain insight into the functional impact of DNA methylation changes, CD Genomics provides comprehensive functional annotation and interpretation of results.
Oxidative Bisulfite Sequencing (oxBS-Seq) Analysis Content:
| Sequencing Data Quality Control |
Ensure thorough data pre-processing and quality control steps to ensure reliable and accurate analysis. |
| Comparison with Reference Genome |
Compare processed oxBS-seq reads to the reference genome. |
| Genome-Wide Methylation and Hydroxymethylation Level Distribution |
Uses sophisticated algorithms and statistical models to determine the methylation levels of individual cytosines, enabling the generation of genome-wide DNA methylation profiles. |
| Differential Methylation and Differential Hydroxymethylation Analysis |
Can reveal regulatory differences associated with various biological processes, developmental stages, or disease states. |
| Functional Annotation Using GO/KEGG |
Involves correlating differentially methylated regions with gene annotation, transcription factor binding sites, regulatory elements and pathway analysis. |
| Differential Expression Levels of Peak-Associated Genes Analysis |
Identifies genes with significant changes in expression levels associated with the presence or absence of peaks in specific genomic regions. |
How It Works
CD Genomics is a high-tech company specializing in multiomic data analysis. We provide services such as project design, data analysis, and database construction. With a focus on developing breakthrough products and services, we are a pioneer in the biotechnology industry, serving researchers and partners worldwide.
CD Genomics offers comprehensive oxBS-seq bioinformatics analysis services to provide accurate interpretation of oxBS-seq data, providing valuable insights into various biological processes, disease mechanisms, and environmental influences. If you are interested in our services, please contact us for more detailed information.
Reference
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Booth MJ, Ost TW, Beraldi D, et al. Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Nat Protoc. 2013 Oct;8(10):1841-51.
