Molecular lab

This molecular lab serves as a cutting-edge S1 facility dedicated to genetic engineering and molecular discovery. By integrating advanced tools—from Next-Generation Sequencing (NGS) and microfluidic electrophoresis to single-cell dissociation—we bridge the gap between complex biological samples and high-resolution genetic data. Our facility provides the essential infrastructure for innovative research within a secure biosafety environment.

DNA Sequencing

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The Illumina MiniSeq is a benchtop next-generation sequencing (NGS) system used to determine the nucleotide sequence of DNA or RNA libraries. It operates using Illumina’s sequencing-by-synthesis (SBS) chemistry, where fluorescence-labeled nucleotides are incorporated one base at a time and detected optically. The system performs cluster generation directly on a flow cell and supports paired-end sequencing (e.g., 2 × 150 bp). It is typically used for targeted gene panels, small genome sequencing, amplicon sequencing, and small RNA sequencing, with output suited for small to medium-throughput projects.

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The Agilent 2100 Bioanalyzer is a microfluidics-based automated electrophoresis instrument used for quality control of DNA, RNA, and proteins. It uses disposable chips containing microchannels where electrophoretic separation occurs with minimal sample input (typically 1 µL). For RNA analysis, it generates an RNA Integrity Number (RIN) to assess sample degradation, which is critical before RNA-seq. It also provides precise fragment sizing and concentration estimation for NGS libraries, displaying results as electropherograms and virtual gel images.

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The NanoDrop 1000 is a microvolume UV-Vis spectrophotometer for rapid quantification of nucleic acids and proteins. It measures absorbance at specific wavelengths (e.g., 260 nm for nucleic acids, 280 nm for proteins) using only 1–2 µL of sample without cuvettes. It calculates concentration and provides purity ratios such as A260/A280 and A260/A230 to detect contamination (e.g., proteins, phenol, salts). It is commonly used immediately after nucleic acid extraction to quickly assess yield and purity before downstream applications.

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The Qubit 2.0 Fluorometer quantifies DNA, RNA, and protein using fluorescent dyes that selectively bind to specific molecule types. Unlike absorbance-based methods, it does not detect free nucleotides or contaminants, making it more accurate for low-concentration or impure samples. The system requires preparation of dye working solutions and standards for calibration. It is particularly important for next-generation sequencing library quantification, where precise DNA concentration is critical for optimal cluster density.

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Conventional PCR machines (thermal cyclers) amplify specific DNA fragments by cycling temperature profiles. A gradient function allows simultaneous testing of multiple annealing temperatures across the block to optimize primer specificity and efficiency. Real-Time PCR (qPCR) instruments incorporate fluorescence detection systems to monitor amplification during each cycle using intercalating dyes (e.g., SYBR Green) or sequence-specific probes. This enables quantification of gene expression, viral load, copy number variation, or mutation detection in real time.

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The Biometra agarose gel electrophoresis system separates nucleic acids based on size by applying an electric field across an agarose matrix. DNA fragments migrate toward the anode, with smaller fragments moving faster through the gel pores. After electrophoresis, DNA is visualized using fluorescent dyes under UV illumination and documented using a gel imaging system. It is typically used to verify PCR products, confirm restriction digests, and assess DNA integrity before cloning or sequencing.

Bio-Rad’s isoelectric focusing (IEF) system separates proteins according to their isoelectric point (pI) within an immobilized pH gradient strip. Proteins migrate under an electric field until they reach the pH at which their net charge is zero. IEF is often used as the first dimension in two-dimensional gel electrophoresis, followed by SDS-PAGE for separation by molecular weight. This approach enables high-resolution analysis of protein isoforms and post-translational modifications in proteomics studies

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The gentleMACS Dissociator is an automated mechanical tissue dissociation system used to generate single-cell suspensions from solid tissues. It uses pre-programmed mechanical disruption protocols in combination with enzyme digestion, depending on the application. The closed-tube system reduces contamination risk and improves reproducibility between samples. It is widely used prior to flow cytometry, single-cell sequencing, or primary cell culture.

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The 10x Chromium Controller enables high-throughput single-cell analysis using microfluidic technology. It encapsulates individual cells into oil droplets, each containing barcoded oligonucleotides. This allows each cell’s RNA or chromatin fragments to receive a unique barcode during library preparation. The system is primarily used for single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics workflows.

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A sterile workbench provides a controlled, particle-free environment for handling sensitive biological materials. HEPA-filtered air flows in a laminar (unidirectional) pattern to prevent airborne contamination of samples. It is commonly used for cell culture, preparation of sterile media, and molecular biology workflows. It may protects the sample, the user, and the environment.