ChIP-Seq

ChIP-Seq (Chromatin Immunoprecipitation Sequencing) is a powerful technique used to analyze protein-DNA interactions on a genome-wide scale. It combines chromatin immunoprecipitation with next-generation sequencing to identify binding sites of DNA-associated proteins, such as transcription factors and histones. This method helps uncover regulatory elements controlling gene expression and epigenetic modifications.

A major focus of the course is on peak calling, where students will learn how statistical algorithms identify regions of the genome enriched with protein binding. They will understand the importance of distinguishing true biological signals from background noise and how to manage multiple testing corrections. The course also explores different file formats used to store and visualize ChIP-Seq data, enabling participants to navigate various bioinformatics tools effectively.

IMG
Learn how to analyze ChIP-Seq data from raw sequencing to biological interpretation. Gain skills in quality control, aligning reads to the genome, identifying binding sites, and annotating genomic regions. Understand how to detect differences between samples, discover DNA motifs, visualize data effectively, and perform pathway analysis to reveal biological functions.

👉 Enroll now and take the first step toward a future in data-driven biology and beyond.

## 10% Discount if you register before 15th October, 2025. Hurry up!!

  • RNASeq [R]
  • RNASeq [D]
  • scRNA-Seq
  • lncRNA-Seq
  • miRNA-Seq
  • PSI-Seq
  • ChipSeq
  • ATAC-Seq
  • scATA-Seq
  • Spatial Transcriptome
  • DNASeq
  • MethylSeq
  • Whole Genome de novo Assembly
  • Targeted metagenomics
  • Whole Genome Metagenomics
  • Metatranscriptomics
  • RAD-Seq
  • SNAP-ChIP

Course Information
Course Chip-Seq (DNA-Protein binding/histone modification)
Duration online 7 Days Training [ 2 Hours Daily [ Monday To Friday ] ]

Slots

Our working Time is 9:00 AM to 6:00 PM Indian Time Available slots - 9:00 AM to 11:00 AM / 11:00 AM to 1:00 PM / 2:00 PM to 4:00 PM / 4:00 PM to 6:00 PM
For training slots after 6 PM or before 9 am as well as weekends training kindly mention during registration accordingly it will be scheduled.

Mode

👉 For online training candidate have to install ZOOM (with remote control on candidate system which makes 100% interactive)
👉 Run time video recording candidate can make as well as pdf manual will be provided for future reference.
👉 All our training is 100% practical and 100% industrial and 100% interactive which provides same as offline learning.
👉 For doubt clear there will be extra support will be provided based on the requirement.
👉 Certificate will be provided
Sequencing Platform Illumina
Raw data Candidate can include maximum 4 datasets of their own during training. Publication standards figures and tables will be generated.
Training Fees
Module-NGS ChipSeq Data Analysis
    📘 Introduction to Bioinformatics & NGS
    - What is Bioinformatics?
    - NGS Technologies Overview
    - Introduction to ATAC-Seq & Applications
    - Paired-end Reads, Tn5 Insertion Bias & ATAC-Seq Algorithm

    📘 Linux Basics & Environment Setup
    - Linux Command Line Basics
    - Installing Tools (FastQC, Bowtie2, MACS2, etc.)
    - Using Conda and Shell Scripting

    📘 Data Retrieval & Formats
    - Fetching data from NCBI SRA using SRA Toolkit
    - Understanding FASTQ, SAM, BAM, BED, GTF formats

    📘 Read Quality Control
    - Check raw data quality and duplication
    - Assess signal quality

    📘 Read Alignment
    - Map reads to the reference genome

    📘 Peak Calling
    - Identify enriched DNA-binding regions
    - Distinguish true signals from noise

    📘 File Formats
    - Work with aligned data (SAM/BAM)
    - Handle peak files (narrowPeak, bedGraph, BigWig)

    📘 Introduction to R/Bioconductor
    - Installing packages with CRAN and Bioconductor
    - Data types and standardized data container
    - Data manipulation

    📘 Annotation
    - Assign peaks to genomic features like promoters or exons

    📘 Differential Binding
    - Identify regions with significant binding differences using edgeR or DESeq2

    📘 Motif Analysis
    - Discover DNA sequence motifs in peaks

    📘 Visualization
    - Use genome browsers (IGV, UCSC)
    - Visualize results with R packages

    📘 Pathway Analysis
    - Analyze gene sets linked to peaks for enriched pathways using KEGG, PantherDB, or ShinyGO

Preparation

- ChIP-seq : https://en.wikipedia.org/wiki/ChIP_sequencing
- NCBI : https://pmc.ncbi.nlm.nih.gov/articles/PMC4151291/

Instructor

Industry Experienced

Target Audiance

This course is designed for graduate students, postdoctoral researchers, and professionals working in the fields of conservation biology, evolutionary genomics, and population genetics or any life sciences who are interested in applying genomic tools to real-world conservation challenges.

Contact

Please write us at info@arraygen.com or call or whatsapp us on mobile +91-9673625446 if you need any clarification or for any custom training based on candidate reference paper or candidate own content/tools.

Course Information
Course Chip-Seq (DNA-Protein binding/histone modification)
Duration online 15 Days Training [ 2 Hours Daily [ Monday To Friday ] ]

Slots

Our working Time is 9:00 AM to 6:00 PM Indian Time Available slots - 9:00 AM to 11:00 AM / 11:00 AM to 1:00 PM / 2:00 PM to 4:00 PM / 4:00 PM to 6:00 PM
For training slots after 6 PM or before 9 am as well as weekends training kindly mention during registration accordingly it will be scheduled.

Mode

👉 For online training candidate have to install ZOOM (with remote control on candidate system which makes 100% interactive)
👉 Run time video recording candidate can make as well as pdf manual will be provided for future reference.
👉 All our training is 100% practical and 100% industrial and 100% interactive which provides same as offline learning.
👉 For doubt clear there will be extra support will be provided based on the requirement.
👉 Certificate will be provided
Sequencing Platform Illumina /Ion Torrent/PacBio/Nanopore
Raw data Candidate can include maximum 4 datasets of their own during training. Publication standards figures and tables will be generated.
Training Fees
Module-I Advanced Bioinformatics & basic programming
Topics
    📘 Introduction to Bioinformatics
    - Overview of bioinformatics and its applications
    - Key concepts in computational biology
    - Role of bioinformatics in genomics, transcriptomics, and proteomics

    📘 Understanding NGS and Genomics Bioinformatics
    - Basics of Next-Generation Sequencing (NGS)
    - Types of NGS data (RNA-seq, WGS, WES)
    - Overview of NGS data formats: FASTQ, BAM, VCF
    - Introduction to pipelines and tools for NGS data analysis

    📘 Databases & Data Retrieval (NCBI and UCSC)
    - Learning how to retrieve biologically correct data
    - Performing complete batch retrieval (e.g., whole exome)
    - NCBI: understanding gene-level data retrieval
    - UCSC: handling large-scale data retrieval
    - UCSC Genome Browser and Table Browser usage
    - Batch Coordinate Retrieval and Genomic Data downloads
    - GFF/GTF gene annotation formats and how to retrieve them
    - Using BLAT for sequence-based search and alignment

    📘 Gene Prediction and Functional Annotation
    - Gene prediction approaches and tools
    - Functional annotation using Gene Ontology (GO)
    - Pathway analysis using KEGG, Reactome
    - Interpreting gene sets and biological relevance

    📘 Standalone/Offline BLAST for Large-Scale Genomic Data
    - Installing and setting up standalone BLAST
    - Running local BLAST for batch sequence alignment
    - Applications in genome-wide homology searches
    - Custom BLAST databases and performance optimization

    📘 PCR Primer Designing and Specificity Check
    - Designing accurate primers for PCR amplification
    - Tools: Primer3, NCBI Primer-BLAST
    - Checking primer specificity using genome-wide BLAST
    - Avoiding non-target amplification through design best practices

    📘 Understanding Python Programming
    - Introduction to Python for bioinformatics
    - Scripting basics: variables, loops, functions
    - Libraries like Biopython, pandas for biological data handling
    - Automating genomic workflows with Python scripts
AND
Module-II Next Generation Sequencing (NGS) - ChipSeq Data Analysis
Topics
    📘 Introduction to Bioinformatics & NGS
    - What is Bioinformatics?
    - NGS Technologies Overview
    - Introduction to ATAC-Seq & Applications
    - Paired-end Reads, Tn5 Insertion Bias & ATAC-Seq Algorithm

    📘 Linux Basics & Environment Setup
    - Linux Command Line Basics
    - Installing Tools (FastQC, Bowtie2, MACS2, etc.)
    - Using Conda and Shell Scripting

    📘 Data Retrieval & Formats
    - Fetching data from NCBI SRA using SRA Toolkit
    - Understanding FASTQ, SAM, BAM, BED, GTF formats

    📘 Read Quality Control
    - Check raw data quality and duplication
    - Assess signal quality

    📘 Read Alignment
    - Map reads to the reference genome

    📘 Peak Calling
    - Identify enriched DNA-binding regions
    - Distinguish true signals from noise

    📘 File Formats
    - Work with aligned data (SAM/BAM)
    - Handle peak files (narrowPeak, bedGraph, BigWig)

    📘 Introduction to R/Bioconductor
    - Installing packages with CRAN and Bioconductor
    - Data types and standardized data container
    - Data manipulation

    📘 Annotation
    - Assign peaks to genomic features like promoters or exons

    📘 Differential Binding
    - Identify regions with significant binding differences using edgeR or DESeq2

    📘 Motif Analysis
    - Discover DNA sequence motifs in peaks

    📘 Visualization
    - Use genome browsers (IGV, UCSC)
    - Visualize results with R packages

    📘 Pathway Analysis
    - Analyze gene sets linked to peaks for enriched pathways using KEGG, PantherDB, or ShinyGO

Preparation

- ChIP-seq : https://en.wikipedia.org/wiki/ChIP_sequencing
- NCBI : https://pmc.ncbi.nlm.nih.gov/articles/PMC4151291/

Instructor

Industry Experienced

Target Audiance

This course is designed for graduate students, postdoctoral researchers, and professionals working in the fields of conservation biology, evolutionary genomics, and population genetics or any life sciences who are interested in applying genomic tools to real-world conservation challenges.

Contact

Please write us at info@arraygen.com or call or whatsapp us on mobile +91-9673625446 if you need any clarification or for any custom training based on candidate reference paper or candidate own content/tools.