Genomics and Proteomics facility

[I] Sample Preparation

Sonicator / Tissue Homogenizer:

  •  Efficient for cell lysis, protein extraction, and tissue homogenization.
  •  Ensures uniform sample preparation for accurate molecular profiling.
  •  Critical for downstream proteomic and genomic analyses.
     
  1. Microcentrifuge: For small volume sample processing. 
  •  Used for high-speed spinning of small samples, typically in microcentrifuge tubes.
  •  Essential for pelleting cells, nucleic acids, or proteins during sample preparation.
  •  Helps separate components based on density for downstream analysis like PCR, RNA extraction, and protein assays
  1. High-Speed Centrifuge: For larger volume samples. 
  • Designed for large-volume samples, enabling high-speed separations in bigger tubes.
  • Ideal for pelleting cellular organelles, isolating subcellular fractions, and density gradient centrifugation.
  • Crucial for applications in purification of proteins, virus particles, and nucleic acid isolation.
  1. Spectrophotometer (NanoDrop)
  • Used for quick and accurate measurement of nucleic acid and protein concentrations in small sample volumes (1-2 µL).
  • Ideal for DNA/RNA quantification and assessment of purity (260/280 nm ratio).
  • Requires no cuvettes, making it highly convenient for high-throughput analysis.
  1. Fluorometer (Qubit)
  • Used for precise quantification of nucleic acids (DNA, RNA) and proteins using fluorescent dyes.
  • Provides high sensitivity and selectivity, minimizing interference from contaminants.
  • Ideal for low-concentration samples, offering greater accuracy than spectrophotometers.
  1. TapeStation
  •  Provides rapid and automated analysis of nucleic acids (DNA/RNA) through gel-like electrophoresis on a chip.
  • Delivers high-resolution size distribution and quality assessment for RNA/DNA integrity.
  •  Ideal for quantifying and assessing the purity of RNA/DNA before downstream applications like sequencing or PCR.
  1. Plate Reader
  • Used for high-throughput analysis of absorbance, fluorescence, and luminescence in multi-well plates.
  • Ideal for quantifying enzymes, protein interactions, cell viability, and assessing gene expression.
  • Enables automated, large-scale screenings, making it suitable for applications in drug discovery and assay development.
     

[II] PCR & Amplification      

  1. Thermocycler (PCR Machine): For DNA amplification. 
  • Used for DNA amplification through Polymerase Chain Reaction (PCR).
  • Enables high-fidelity amplification of specific DNA regions for applications like gene cloning, mutagenesis, and genetic analysis.
  • Provides precise temperature control for denaturation, annealing, and extension steps in PCR.
     
  1. Real-Time PCR (qPCR) System:      
  • Used for quantitative analysis of gene expression and DNA quantification in real-time.
  • Measures amplification during each PCR cycle using fluorescent dyes or probes, providing quantitative data.
  • Ideal for detecting low-abundance targets, viral load quantification, and gene expression profiling.
  1. Electrophoresis System:  Horizontal and Vertical (small, standard and long)
  • Used for separating nucleic acids (DNA/RNA) or proteins based on size and charge through an electric field.
  • Horizontal electrophoresis is typically used for agarose gel electrophoresis (for DNA/RNA separation), while vertical electrophoresis is used for polyacrylamide gels (for protein separation).
  • Available in small, standard, and long formats to accommodate different sample volumes and gel sizes, enabling high-resolution separation.
  1. Gel Documentation System: For imaging DNA RNA and protein.
  • Used for capturing high-resolution images of gel electrophoresis results for DNA, RNA, and protein analysis.
  • Equipped with a camera and light source (UV or LED) for visualizing fluorescent or chemiluminescent stains.
  • Provides quantitative and qualitative data on gel bands, enabling accurate size determination and concentration analysis.
     

[III] Next-Generation Sequencing (NGS) & High-Throughput Genomics      

  1. NGS Sequencer (MGI sequencer)
  • Used for high-throughput sequencing of DNA/RNA to generate large-scale genomic data.
  • Capable of performing whole genome sequencing, RNA sequencing, and targeted sequencing with high accuracy and sensitivity.
  • Provides fast, scalable, and cost-effective sequencing solutions, ideal for genomic research, biomarker discovery, and clinical diagnostics.
  1. Oxford Nanopore
  • Provides real-time, long-read sequencing of DNA/RNA with the ability to sequence native DNA without amplification.
  • Uses nanopore technology to detect changes in electrical conductivity as molecules pass through a pore, offering high accuracy and scalability.
  • Ideal for applications requiring long-read sequencing, such as genome assembly, structural variant detection, and metagenomics.

[IV] Bioinformatics & Data Analysis

  • High-Performance Computing (HPC) Server
  • Workstations with Genome Analysis Softwares

[V] Protein Separation & Characterization

  1. FPLC
  • Fast Protein Liquid Chromatography (FPLC) is used for purifying proteins and other biomolecules based on their size, charge, or affinity.
  • Offers high-resolution separation with precise control over flow rates and gradients, making it ideal for protein purification and enzyme analysis.
  • Commonly used in biotechnology and pharmaceutical industries for purification of recombinant proteins, antibodies, and enzymes.

[VI] High-Throughput Proteomics and structure

  1. Mass spectrometry
  • Used for identifying and quantifying molecules based on their mass-to-charge ratio, essential for proteomics, metabolomics, and lipidomics.
  • Enables detailed analysis of complex mixtures, allowing for the detection of proteins, peptides, small molecules, and post-translational modifications.
  • Provides high sensitivity and accuracy, making it ideal for biomarker discovery, drug development, and structural analysis of biomolecules.