Suite16

Suite16 analyzes and visualizes matrix attachment regions (MARs) in genomic sequences, focusing on human chromosome 16 to determine MAR distribution and support studies of chromatin organization and gene regulation.

Key Features:

• Co-localization and Visualization: Provides visualization and co-localization of genomic features including MARs to assess their spatial organization within the genome.
• Platform Evaluation: Evaluates cosmid and oligonucleotide arrays for MAR identification and assesses their performance using quantitative real-time PCR (Q-PCR) to ensure accurate representation of non-coding regions.
• Extraction Protocol Analysis: Analyzes the impact of extraction protocols, including lithium di-iodosalicylic acid (LIS) and NaCl, on MAR detection and representation.
• High-throughput MAR Determination: Utilizes high-throughput technologies to enable direct determination of MAR distribution across genomes.

Scientific Applications:

• Systems Biology Mapping: Defines the role and distribution of MARs across different cell types in systems biology studies.
• Gene Regulation and Chromatin Organization: Investigates MAR involvement in gene regulation and chromatin organization.
• Platform and Protocol Assessment: Compares array platforms and extraction protocols to refine experimental designs and improve genomic study accuracy.

Methodology:

Analysis uses high-throughput technologies to determine MAR distribution and incorporates quantitative real-time PCR (Q-PCR) for validation while evaluating the effects of extraction protocols such as lithium di-iodosalicylic acid (LIS) and NaCl.