ChIP Sequencing

Chromatin Immunoprecipitation (ChIP) coupled with next generation sequencing as a detection method (ChIP-seq) has become one of the primary methods to discover genome wide protein-DNA interaction. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.


In ChIP-Seq, enriched DNA regions (protein binding sites) are detected as peaks above background reads, and bioinformatics analyses of these regions can reveal binding motifs. Applications include studies on gene regulation, transcription complex assembly, histone modification, developmental mechanisms, and disease processes.

The major steps in ChIP Sequencing are given below:

  • Chromatin preparation: cell fixation (cross-linking) of chromatin-bound proteins such as histones or transcription factors to DNA followed by cell lysis.
  • Chromatin shearing: fragmentation of chromatin by sonication down to desired fragment size (100-500 bp).
  • Chromatin IP: protein-DNA complexe capture using specific ChIP-seq grade antibodies against the histone or transcription factor of interest.
  • DNA purification: chromatin reverse cross-linking and elution followed by purification.
  • NGS Library Preparation: adaptor ligation and amplifcation of IP’d material.
  • Sequencing: Sequencing on Illumina platform, generally single-end 50bp read length is suitable for ChIP Sequencing.
  • Bioinformatic analysis: read filtering and trimming, read specific alignment, enrichment specific peak calling, QC metrics, multi-sample cross-comparison etc.

Whole Genome Bisulfite Sequencing

In India, Nucleome Informatics has most experienced scientitsts to sequence and analyse epigenome by Whole genome bisulfite sequencing method. The DNA contains combinations of four nucleotides which include cytosine, guanine, thymine and adenine. DNA methylation refers to the addition of a methyl (CH3) group to the DNA strand itself, often to the fifth carbon atom of a cytosine ring. This conversion of cytosine bases to 5-methylcytosine is catalysed by DNA methyltransferases (DNMTs).  These modified cytosine residues usually lie next to a guanine base (CpG methylation) and the result is two methylated cytosines positioned diagonally to each other on opposite strands of DNA.


DNA methylation at the C5 position of cytosine plays a crucial role in gene expression and chromatin remodelling, and perturbations in methylation patterns are implicated in the development of cancer, neurodegenerative diseases, and neurological disorders. Therefore, the mapping of methylated bases (the methylome) is critical to understanding gene expression and other processes subject to epigenetic regulation.


Nucleome provides whole genome sequencing of bisulfite-converted DNA, as an effective method to identify individually methylated cytosines on a genome-wide scale. Methylome analysis is an increasingly valuable research tool with a range of applications, including studies on gene regulation, stem cell differentiation, embryogenesis, aging, cancer and other diseases, and phenotypic diversity and evolution in plants and animals. We recommend Paired end 150 bp sequencing of 250~300-bp insert bisulfite treated DNA library on HiSeq system. We provide a comprehensive data analysis report which includes raw data QC, alignment, Motif analysis, DMR etc. For more information visit Bioinformatics analysis page. We also offer ‘Reduced Representation Bisulfite Sequencing’ to determine the methylation in economical way. We have performed WGBS and data analysis in human, mouse, rice, wheat, horsegram, tobacco and many other species. We provide extensive support in strategy, project design, sample preparation, methylome sequencing (WGBS) and data analysis to Indian and international clients.

Infinium MethylationEPIC v2.0 

Our cutting-edge genomics service brings you the revolutionary Infinium MethylationEPIC v2.0 BeadChip Kit, a genome-wide methylation screening tool designed to unlock the hidden secrets of the human methylome. With a focus on the most biologically significant regions, this state-of-the-art kit targets over 935,000 CpG sites, empowering you with comprehensive insights into DNA methylation patterns.

Unparalleled Precision and Compatibility

Built on the solid foundation of its predecessor, MethylationEPIC v1.0, this advanced array ensures maximum backward compatibility. The Infinium MethylationEPIC v2.0 BeadChip Kit maintains the exceptional ability to quantitatively interrogate CpGs across the genome with single-nucleotide resolution. What’s more, it provides highly accurate and precise methylation measurements independently of read depth, ensuring you can trust your results with confidence.

Streamlined, User-Friendly Analysis

At Nucleome Informatics, we understand the importance of efficiency and ease-of-use in genomics research. That’s why we’ve streamlined the entire process. Our Infinium Methylation assay allows you to analyze multiple DNA sample types, including those isolated from FFPE, without any hassle. Its user-friendly interface ensures that you can focus on your research, not the technicalities.

Empowering Groundbreaking Research

MethylationEPIC v2.0’s scalability and low total cost per sample make it the ideal choice for large cohorts and studies. With our genomics service, you can screen vast sample sets to uncover powerful biological insights into disease mechanisms. From unraveling disease pathways to identifying potential therapeutic targets, the potential for groundbreaking discoveries is within your reach.

Why Choose Nucleome Informatics?

Nucleome Informatics is committed to providing cutting-edge genomics solutions that empower researchers and clinicians alike. With our expertise in genomics and bioinformatics, we offer comprehensive support throughout your research journey. We are dedicated to helping you make meaningful advancements in the field of genomics, and the Infinium MethylationEPIC v2.0 BeadChip Kit is just one of the many ways we achieve that goal.

Join the genomics revolution and uncover the hidden mysteries of the methylome with Nucleome Informatics’ Infinium MethylationEPIC v2.0 BeadChip Kit. Contact us today to learn more about our services and how we can help drive your research forward. Together, let’s decode the language of DNA and shape a brighter future for healthcare and beyond.

Key Benefits of Nucleome Informatics’ Twist Human Methylome Panel:

  1. Design and Workflow Efficiency: Experience a seamless and efficient research journey from start to finish.
  2. Optimized Performance: Achieve unmatched performance with our integrated end-to-end workflow.
  3. Increased Library Complexity: Elevate your sequencing data quality with enhanced library complexity.
  4. Flexibility in Content: Customize your research with the option to add spike-in content for tailored analysis.
  5. Broader Coverage: Surpass the limitations of average microarrays with ~4x more coverage of all CpG sites.
  6. More Coverage of CpG Islands: Get detailed insights with enhanced coverage of CpG island bases.
  7. Updated Reference Databases: Rely on the latest information for your research, backed by updated reference databases.
  8. Advantage over Microarrays: Enjoy higher calls at differentially methylated regions and increased coverage of adjacent CpG sites upstream and downstream.

Join the Epigenetic Revolution with Nucleome Informatics

At Nucleome Informatics, we are dedicated to empowering researchers like you with cutting-edge solutions. Explore the intricate world of epigenetics with the Twist Human Methylome Panel and uncover the hidden language of DNA methylation. Contact us today to learn more about our services and how we can propel your research forward. Together, let’s make history in the realm of epigenetics.

Explore the Epigenetic Landscape with Nucleome Informatics’ Twist Human Methylome Panel

Welcome to Nucleome Informatics’ Methylome Sequencing Service, where we bring you the transformative Twist Human Methylome Panel – an exceptional tool designed to unravel the complexities of DNA methylation. With precision targeting of 3.98 million CpG sites across 123 megabases of genomic content, this panel homes in on biologically relevant methylation markers, opening up a world of possibilities for investigators across diverse applications.

Comprehensive Coverage for In-Depth Analysis

Nucleome Informatics’ Twist Human Methylome Panel boasts expansive content, making it the perfect choice for investigating the methylation fraction in a wide range of areas, including cancer metastasis, human development, and functional genomics. No matter your research focus, this panel provides the depth and breadth of information you need to make groundbreaking discoveries.

Seamless Integration with Twist Methylation Detection System

Our panel is fully optimized and rigorously validated for use with the Twist methylation detection system, offering you a complete end-to-end workflow with industry-leading performance. Experience enhanced capture efficiency, elevating the sensitivity of detection across the entire epigenome footprint while simultaneously reducing sequencing costs. Say goodbye to unnecessary complexities and focus on what truly matters – advancing your research.

Empowering Cohort Studies and Discovery

Nucleome Informatics’ Twist Human Methylome Panel is a game-changer for screening cohort samples and identifying differentially methylated regions. With its robust performance, it accelerates your research and delivers valuable insights into the dynamic world of DNA methylation. Unlock the hidden potential of epigenetics and pave the way for novel discoveries that can shape the future of medicine and beyond.

Reduced Representation Bisulfite Sequencing on NovaSeq 6000 with Data Analysis by Nucleome Informatics

Service Description: Nucleome Informatics is proud to offer a cutting-edge Reduced Representation Bisulfite Sequencing (RRBS) service on the state-of-the-art NovaSeq 6000 platform. RRBS is a highly specialized technique used for DNA methylation analysis, enabling researchers to investigate the epigenetic modifications that play a crucial role in gene regulation and various biological processes.

Service Features:

  1. High-Quality RRBS Sequencing: We utilize the Illumina NovaSeq 6000 sequencer, renowned for its precision and scalability, to provide high-quality sequencing data. This platform ensures accurate and comprehensive DNA methylation profiling.
  2. Sample QC and Preparation: Our experienced team assists you in sample quality control, DNA extraction, bisulfite conversion, and library preparation, ensuring that your samples are prepared to the highest standards.
  3. Reduced Representation: RRBS targets CpG-rich regions in the genome, focusing on regions of high biological significance, such as gene promoters and enhancers. This reduces sequencing costs while providing valuable insights into DNA methylation.
  4. Customized Experimental Design: We work closely with you to tailor the RRBS experiment to your specific research needs, helping you select the most relevant genomic regions for analysis.
  5. Data Analysis by Nucleome Informatics: Our bioinformatics experts are well-versed in handling RRBS data. We offer comprehensive data analysis, including:
    • Quality Control: Ensuring data integrity and reliability through stringent quality control measures.
    • Read Mapping: Accurate alignment of sequenced reads to the reference genome.
    • DNA Methylation Calling: Quantifying DNA methylation levels at individual CpG sites.
    • Differential Methylation Analysis: Identifying significant methylation differences between samples or conditions.
    • Visualization: Generating intuitive visualizations and reports to aid in data interpretation.
    • Biological Interpretation: Providing insights into the biological implications of your DNA methylation data.
  6. Data Delivery: We deliver analysis results in a format that is easy to interpret and integrate into your research. You will receive detailed reports, figures, and raw data files for further exploration.
  7. Data Security and Confidentiality: We prioritize the security and confidentiality of your data. Our systems and practices adhere to the highest standards of data protection.

Benefits of Choosing Nucleome Informatics:

  • Expertise: Our team consists of experienced scientists and bioinformaticians who are well-versed in RRBS and epigenetics research.
  • Cutting-Edge Technology: We employ the latest sequencing technology to ensure the highest data quality and accuracy.
  • Customized Solutions: We understand that each research project is unique, and we tailor our services to meet your specific requirements.
  • Data Interpretation: Our data analysis goes beyond raw numbers; we provide meaningful insights into your epigenetic data.
  • Timely Results: We strive to deliver results promptly, allowing you to move forward with your research efficiently.

Unlock the potential of your epigenetic research with Nucleome Informatics’ RRBS service on the NovaSeq 6000 platform. Contact us today to discuss your project and how we can help you gain deeper insights into DNA methylation patterns.

Understanding ATAC-Seq: Unveiling the Chromatin Landscape

Unlock the secrets of the chromatin landscape with India’s trusted genomics research partner Nucleome Informatics. Contact us today to embark on your journey of ATAC-Seq services. ATAC-Seq, or the Assay for Transposase-Accessible Chromatin with Sequencing, is a revolutionary method for exploring chromatin accessibility throughout the genome. This cutting-edge technique allows researchers to delve into the intricate world of gene expression regulation by identifying regions of open chromatin.

How ATAC-Seq Works:
In ATAC-Seq, genomic DNA is exposed to Tn5, a highly active transposase. Tn5 serves a triple role: it fragments DNA, inserts into open chromatin sites, and adds sequencing primers through a process called tagmentation. The resulting sequenced DNA provides valuable insights into the regulatory elements of the genome, facilitating the study of gene expression regulation.

Applications of ATAC-Seq:
The versatility of ATAC-Seq extends to various domains of research, including:

– Nucleosome mapping
– Transcription factor binding analysis
– Identification of novel enhancers
– Exploring disease-relevant regulatory mechanisms
– Cell type–specific regulation analysis
– Evolutionary studies
– Comparative epigenomics
– Biomarker discovery

Coverage Recommendations:
The depth of sequencing coverage required for ATAC-Seq depends on the specific research goals. Here are some recommended coverage depths for common applications:

– Identification of open chromatin differences in human samples: ≥ 50 M paired-end reads
– Transcription factor footprinting for constructing gene regulatory networks: > 200 M paired-end reads
– Single-cell analysis: 25–50 K paired-end reads per nucleus/cell

Why Paired-End Reads?
We recommend using paired-end reads for ATAC-Seq due to their numerous advantages, including higher unique alignment rates, removal of PCR duplicates, more complete information about accessible sequences, and the ability to categorize reads as nucleosome-free, mono-nucleosomal, or di-nucleosomal.

Consultation and Collaboration:
At Nucleome Informatics, we are committed to supporting your research endeavors. Our team of experts is available for consultations to discuss your project requirements and provide tailored solutions. Whether you’re exploring chromatin accessibility in complex diseases or uncovering regulatory mechanisms in developmental biology, we’re here to help you every step of the way.

ATAC-Seq workflow

ATAC-Seq workflow