Open Science & Reproducibility · Bench-Verified SOPs

Laboratory Protocol Collections & SOPs

Standardized, bench-verified protocols developed and utilized by MSI Lab researchers across viral surveillance, clinical serology, in vivo challenge, molecular docking, and phytochemical extractions.

Standardized Operating Procedures & Quality Rigor

Bench-Verified Protocols & Reproducible Science

Peer-reviewed experimental protocols calibrated against clinical samples and verified across dozens of runs for viral RNA isolation, real-time qPCR, recombinant bacterial expression, and indirect ELISA.

Verified
11 SOPs
Bench Tested
Format
DOCX
Open Download
Standard
GLP
Biosafety II
Browse SOPs ↗
Virology & Diagnostics DOCX · 26 KB

1-Step RT-qPCR Mastermix & Amplification Protocol

Standard operating procedure for one-step real-time reverse transcription PCR, covering RNase-free glassware preparation, primer-probe mastermix assembly, and thermal cycling parameters for viral pathogen surveillance.

Standard Operating Procedure (SOP) Highlights:
  • ✓ Baking glassware at 180–200°C for ≥4 hours to destroy RNases
  • ✓ TE buffer & DEPC-treated nuclease-free water preparation
  • ✓ Multiplex primer and hydrolysis probe mastermix formulation
  • ✓ qTOWER³ G linear thermal cycling and threshold baseline calibration
Validated Equipment / Platforms:
Analytik Jena qTOWER³ G qPCR Benchmark SureAir™ PCR Workstation Refrigerated Microcentrifuge
Download Protocol (.DOCX)
Virology & Diagnostics DOCX · 20 KB

Extraction & Purification of Viral RNA from Whole Blood

Phase-by-phase extraction protocol isolating high-purity total and viral genomic RNA from human clinical whole blood samples with beta-mercaptoethanol lysis optimization.

Standard Operating Procedure (SOP) Highlights:
  • ✓ RNA Lysis Buffer (RLA) preparation with β-mercaptoethanol (BME)
  • ✓ Clinical specimen homogenization and cellular disruption
  • ✓ Silica-membrane spin column purification and on-column DNase digestion
  • ✓ Elution in nuclease-free water and A260/A280 spectrophotometric validation
Validated Equipment / Platforms:
Haier Class II Biosafety Cabinet Refrigerated Microcentrifuge Vortex Mixer
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Virology & Diagnostics DOCX · 19 KB

Extraction & Purification of Circulating RNA from Serum

Optimized protocol for recovery of cell-free circulating viral genomic RNA from patient serum samples, calibrated for acute viremic titers in arboviral infections.

Standard Operating Procedure (SOP) Highlights:
  • ✓ Preparation of serum lysis buffers with optimized reducing agents
  • ✓ Inactivation of serum RNases and viral envelope capsid lysis
  • ✓ Alcohol-mediated nucleic acid precipitation and column bind-wash-elute cycles
  • ✓ Direct preservation at -80°C in Cryogenic Specimen Biobank
Validated Equipment / Platforms:
Haier Class II Biosafety Cabinet Cryogenic Biobank (-80°C) Microcentrifuge
Download Protocol (.DOCX)
Virology & Diagnostics DOCX · 19 KB

Extraction & Purification of Total RNA from Murine Spleen Tissue

Specialized protocol detailing tissue mass constraints (≤15 mg) and shear parameters required to prevent high-viscosity lysates when isolating immune lymphoid RNA from immunized mouse spleens.

Standard Operating Procedure (SOP) Highlights:
  • ✓ Strict starting mass limit (≤15 mg spleen tissue) to prevent lysate viscosity overload
  • ✓ Rapid mechanical micro-pestle or bead homogenization in lysis buffer
  • ✓ Viscosity reduction and cellular debris pelleting
  • ✓ RNA purification for downstream cytokine profiling and IgG repertoire sequencing
Validated Equipment / Platforms:
Benchmark Pulse 650 Homogenizer Haier Class II Biosafety Cabinet qTOWER³ G qPCR
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Immunology & Serology DOCX · 58 KB

Indirect ELISA Protocol, Calculations & Serological Data Analysis

Comprehensive guide covering molarity and buffer math (% w/v, mM mass, C1V1=C2V2, RPM vs. RCF), antigen coating, blocking, serial serum dilution, and optical density (OD450) sigmoid curve fitting.

Standard Operating Procedure (SOP) Highlights:
  • ✓ Stock buffer formulation (10x PBS, coating buffer pH 9.6, wash buffer PBST)
  • ✓ Solid-phase antigen coating and BSA/casein blocking optimization
  • ✓ Serial dilution series of clinical plasma or murine immune sera
  • ✓ HRP-conjugated secondary antibody incubation and TMB chromogenic kinetics
  • ✓ OD450 measurement on Microplate Reader and endpoint titer calculation
Validated Equipment / Platforms:
Tecan Infinite 200 PRO Microplate Reader Multichannel Pipettes Borosil Ultrapure Water
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Immunology & Serology DOCX · 21 KB

Flow Cytometry Immunophenotyping & Whole Blood RBC Lysis

Standard flow cytometry procedure for blood sample preparation, red blood cell ammonium chloride lysis, cell suspension washing, fluorophore-conjugated antibody staining, and cytometer gating.

Standard Operating Procedure (SOP) Highlights:
  • ✓ Blood aliquot preparation (20–30 µL) in 10 mL / 5 mL FACS tubes
  • ✓ RBC lysis buffer addition and 5-minute room temperature incubation
  • ✓ Low-speed centrifugation (1600 rpm / 4°C) and pellet washing
  • ✓ Surface antigen antibody fluorophore cocktail staining (CD3/CD4/CD8/CD19)
  • ✓ Acquisition and population gating on BD FACSAria / Beckman CytoFLEX
Validated Equipment / Platforms:
BD FACSAria III Flow Cytometer Refrigerated Centrifuge Euromex BioBlue.Lab
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Immunology & Serology DOCX · 539 KB

In Vivo Murine Immunization, Challenge & Buffer Preparation

Protocol detailing 10x PBS buffer chemistry, antigen-adjuvant formulation, immunization dosing schedules in BALB/c and AG129 mice, and blood/spleen harvesting for vaccine evaluation.

Standard Operating Procedure (SOP) Highlights:
  • ✓ 10x Phosphate-buffered saline (PBS, pH 7.4) preparation (Na2HPO4, NaH2PO4, KCl, NaCl)
  • ✓ Subunit antigen emulsion with nano-adjuvants
  • ✓ Subcutaneous and intramuscular prime-boost vaccination scheduling
  • ✓ Retro-orbital / tail-vein blood collection and aseptic organ harvesting
Validated Equipment / Platforms:
Haier Class II Biosafety Cabinet Animal Biosafety Facility Astec CO₂ Incubator
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Computational Structural Biology DOCX · 26 KB

Antigen-Antibody Docking & Interface Thermodynamics using HADDOCK 2.4

End-to-end computational pipeline for structural preparation in PyMOL/ChimeraX, PDB cleaning, active/passive restraint definition, rigid-body docking, semi-flexible refinement, and PRODIGY binding free energy analysis.

Standard Operating Procedure (SOP) Highlights:
  • ✓ PDB sequence trimming, heteroatom/water removal, and chain renaming in PyMOL
  • ✓ Epitope and paratope CDR loop residue definition (active/passive restraints)
  • ✓ HADDOCK 2.4 webserver parameter configuration (it0, it1, and water refinement)
  • ✓ Cluster analysis, Z-score ranking, and interfacial buried surface area (BSA) calculation
  • ✓ PRODIGY biophysical contact mapping and binding affinity (ΔG / Kd) prediction
Validated Equipment / Platforms:
HADDOCK 2.4 Server PRODIGY Biophysical Suite PyMOL & UCSF ChimeraX High-Performance Workstation
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Plant Molecular Biology DOCX · 6.6 MB

Clonal Propagation of Aquilaria malaccensis via Stem Cuttings

Field-ready protocol developed by the MSI Lab for the vegetative clonal propagation and rooting induction of critically endangered agarwood (Aquilaria malaccensis) stem cuttings.

Standard Operating Procedure (SOP) Highlights:
  • ✓ Donor mother-plant selection and juvenile orthotropic branch harvesting
  • ✓ Nodal cutting preparation, leaf surface area reduction, and anti-fungal washing
  • ✓ Auxin hormone conditioning under humidity-controlled mist propagation chambers
  • ✓ Adventitious rooting monitoring, survival rate quantification, and hardening
Validated Equipment / Platforms:
Plant Growth Suite Rocker 300 Vacuum Pump Mist Propagation Chamber
Download Protocol (.DOCX)
Plant Molecular Biology DOCX · 31 KB

IBA Quick-Dip Hormone Preparation Guide for Stem Cuttings

Preparation guide for synthetic auxin Indole-3-butyric acid (IBA) stock solutions, dissolution chemistry, potassium hydroxide/ethanol co-solvents, and concentration titration for agarwood rooting.

Standard Operating Procedure (SOP) Highlights:
  • ✓ IBA chemical dissolution in absolute ethanol / 1M KOH
  • ✓ Preparation of concentrated stock solutions (1000–5000 ppm)
  • ✓ Basal stem quick-dip exposure timing (5–10 seconds)
  • ✓ Safety precautions and hormone storage longevity protocols
Validated Equipment / Platforms:
Analytical Precision Balance pH Meter Chemical Fume Hood
Download Protocol (.DOCX)
Plant Molecular Biology DOCX · 31 KB

CTAB-Based Total RNA Extraction from Recalcitrant Agarwood Heartwood

Specialized modified CTAB protocol for extracting intact, high-quality total RNA from woody, polyphenol- and polysaccharide-dense Aquilaria malaccensis tissues for terpene synthase RT-qPCR.

Standard Operating Procedure (SOP) Highlights:
  • ✓ Liquid nitrogen grinding of resinous heartwood into ultra-fine powder
  • ✓ Modified CTAB lysis buffer with 2% PVP to bind and precipitate polyphenols
  • ✓ Chloroform:isoamyl alcohol (24:1) phase separation and lithium chloride RNA precipitation
  • ✓ RNA integrity assessment by denaturing agarose gel and RT-qPCR gene expression analysis
Validated Equipment / Platforms:
Liquid Nitrogen Cryocooler Benchmark Pulse 650 Homogenizer qTOWER³ G qPCR
Download Protocol (.DOCX)