(Single-cell) ATAC-Seq

ATAC-Seq: Illuminating the Epigenetic Landscape

Understanding the intricate epigenetic mechanisms that orchestrate gene expression is pivotal in deciphering the complexities of cellular function, differentiation, and identity. Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-Seq) stands at the forefront of this exploration, offering a high-resolution window into the regulatory architecture of the genome.

At IGATech, we specialize in scATAC-Seq to unveil the chromatin accessibility landscape across individual cells, providing insights that are crucial for revealing the nuanced layers of gene regulation. Our approach is twofold, ensuring tailored solutions for diverse research needs:

1. Bulked Approach: By constructing comprehensive ATAC-Seq DNA libraries, we facilitate comparative studies across varied conditions or distinct tissue types, enabling a broad overview of chromatin accessibility dynamics.

1. Single-Cell Resolution: Leveraging the advanced Chromium system by 10X Genomics, we offer single-cell ATAC-Seq services, capturing the chromatin accessibility profile of thousands of cells in a single run. This method empowers researchers to dissect heterogeneity within cell populations, identify rare cell types, and uncover regulatory variations that drive disease progression and cellular development.

Our expertise extends beyond data generation. We support our clients through every step of the experimental journey, from designing robust studies to interpreting complex datasets. Our bioinformaticians employ state-of-the-art algorithms and custom analytical workflows to extract meaningful biological insights from your data.

By choosing IGATech for your scATAC-Seq needs, you benefit from:

• Expertise: Our seasoned scientists bring a wealth of experience in epigenetics and genomics.
• Flexibility: We cater to both large-scale and targeted studies, ensuring your research questions are comprehensively addressed.
• Support: From experimental design to data analysis, we offer continuous support tailored to your research goals.
• Innovation: Stay at the cutting edge with our technologically advanced platforms and analytical tools.

Bioinformatics Analysis Service

Our ATAC-seq analysis service provides a comprehensive workflow for chromatin accessibility profiling, ensuring high-quality data processing, peak identification, and biological insights.

Analysis Workflow

• Preprocessing – Quality control and adapter trimming of raw reads.
• Reads Alignment & Filtering – Choice of multiple aligners (e.g., BWA, Bowtie2, STARenrichment), removal of low-quality and duplicate reads.
• Alignment QC – Evaluation of mapping efficiency and fragment size distribution.
• Enrichment Analysis – Signal quantification at genomic features.
• Peak Calling & Annotation – Identification of accessible chromatin regions and annotation.
• Consensus Peak Set Generation – Merging peaks across replicates for robust comparisons.
• Differential Accessibility Analysis – Identification of differentially accessible regions (DARs) between conditions.
• Comprehensive QC Reporting – Interactive reports summarizing all analysis steps.

Key Deliverables

• Raw & Processed Sequencing Data
  • Raw Sequencing Reads – FASTQ files of unprocessed reads.
  • Quality Control Reports – HTML reports detailing read quality, adapter trimming, and filtering.
• Alignment Data
  • Mapped Reads – BAM files of aligned reads, indexed for easy access.
  • Filtered & Processed Reads – Library-level, coordinate-sorted BAM files with duplicate marking and quality filtering.
• Peak Identification & Annotation
  • Peak Calls – BED files, spreadsheets, and QC plots of identified peaks.
  • Annotated Peaks – Functional annotation of peaks to nearby genes and regulatory elements.
  • Consensus Peak Set – Merged peak regions across samples, with read counts and peak-to-gene assignments.
• Differential Accessibility Analysis
  • Differential Peak Lists – Identified differentially accessible regions (DARs) with fold changes and p-values.
  • Comprehensive Reports – R objects, spreadsheets, and data files for downstream visualization and integration.
• Visualization & Quality Control
  • Aggregated QC Metrics – Summary statistics for raw reads, alignment, peak calling, and differential accessibility.
  • Genome Browser Tracks – Session files (e.g., for IGV, UCSC Genome Browser) for interactive exploration of results.

Embrace the full potential of scATAC-Seq with IGATech as your partner. Together, we can illuminate the epigenetic intricacies of cellular function and unlock the secrets held within the chromatin landscape.

To embark on your scATAC-Seq journey, contact IGATech today. Let's design an experiment that propels your research into new realms of discovery.

Reference Articles:

• "Comprehensive Integration of Single-Cell Data," Cell, 2019. This landmark study showcases the power of single-cell technologies to provide a unified view of cellular complexity and identity.
• "Single-cell chromatin accessibility reveals principles of regulatory variation," Nature, 2015. A foundational paper in the field, demonstrating the utility of scATAC-Seq in understanding individual cell regulatory mechanisms.