Protocols

High-Salt CTAB DNA Extraction

Obtain high-molecular-weight genomic DNA suitable for long-read sequencing or Southern blotting. The protocol combines a...

Genomic-tip 20/G extraction of high-molecular-weight genomic DNA from ≤ 20 mg animal or plant tissue (with Proteinase K & RNase A treatments)

To obtain 15-20 µg of high-quality, 20–150 kb genomic DNA suitable for downstream molecular biology applications from fr...

Nanodrop analysis of nucleic acid concentration and purity

This procedure describes the steps for assessing the concentration and purity of nucleic acids (DNA or RNA) using a Nano...

Serial Dilution of DNA

A standardized method for preparing single and serial dilutions of DNA (e.g., 1:10, 1:100, 1:1000) for downstream assays...

Qubit™ 1X dsDNA HS Assay (High Sensitivity)

To accurately quantify double‑stranded DNA (dsDNA) in the range of 0.2–100 ng total DNA per tube using the Qubit™ 1X dsD...

Femto Pulse – Genomic DNA 165 kb (FP‑1002‑22, 22 cm)

**Purpose** To size and quantify high‑molecular‑weight (HMW) genomic DNA (\~1.3 kb–165 kb) using the Agilent Femto Puls...

EZ DNA Methylation‑Gold™ Kit — Bisulfite Conversion of DNA

### Purpose To convert unmethylated cytosines in DNA to uracil (while preserving 5‑methylcytosine) using the EZ DNA M...

Bisulfite amplicon sequencing library preparation (using TruSeq adapters)

A **complete SOP** for generating **MiSeq‑ready bisulfite amplicon libraries** with **TruSeq‑tailed primers**. It assume...

Ligation sequencing DNA V14 (SQK-LSK114) library preparation and sequencing on MinION

This protocol describes how to carry out sequencing of a DNA sample using the Ligation Sequencing Kit V14 (SQK-LSK114).

DNA extraction of insect tissue using the ZymoBIONICS DNA miniprep kit

This is a column-based DNA extraction procedure that has a PCR inhibitor removal step.

DNA and RNA extraction from insects using the ZymoBIOMICS DNA/RNA miniprep kit

Column-based approach to separately isolate DNA and RNA from the same sample.

Extraction of RNA from yeast using the ZymoBIONICS YeaStar RNA kit

Quick, spin-column purification of total RNA (including small/microRNAs) from a wide range of fungi species, susceptible...

Direct cDNA sequencing V14 with SQK-LSK114

This protocol describes how to carry out sequencing of cDNA using a reverse transcription and strand-switching method an...

Total RNA extraction from animal tissues using PureLink RNA Mini Kit

Standardized procedure to isolate high-quality total RNA from animal tissues using silica spin columns.

Fragment Analyzer – RNA (Eukaryotic)

Run total RNA on the Fragment Analyzer using the eukaryotic RNA analysis mode.

PacBio Iso‑Seq cDNA Preparation — Reverse Transcription, Template Switching, and PCR Amplification and Bead-based Size Binning

A validated procedure to generate amplified cDNA for PacBio Iso‑Seq from total RNA and optional size-binning of PCR‑ampl...

Fragment Analyzer – HS Large Fragment 50Kb

PacBio Iso‑Seq Library Preparation — SMRTBell Ligation

SMRTbell Express Template Prep v2.0 with adapter‑ligation barcodes (ALB)

PacBio Sequel II — Polymerase Binding and Optional Post‑Binding Pooling

Bind Sequel II polymerase to finished SMRTbell Iso‑Seq libraries, optionally pool after binding prior to sequencing on t...

PCR-cDNA Barcoding sequencing library preparation (SQK-PCB111.24)

Oxford Nanopore Technologies PCR-cDNA Barcoding kit (SQK-PCS111) for full-length cDNA library preparation from total RNA...

Ligation sequencing DNA (SQK-LSK109) library preparation

Adapter ligation library prep for nanopore sequencing using the legacy SQK-LSK109 kit.

Direct RNA sequencing (SQK-RNA004) library preparation

Direct RNA nanopore sequencing library preparation using the SQK-RNA004 kit for native RNA strand analysis.

Simultaneous DNA and RNA extraction from animal tissues using QIAGEN AllPrep DNA/RNA Mini Kit

Simultaneous purification of genomic DNA and total RNA from the same tissue sample (≤30 mg) using selective AllPrep DNA ...

Equimolar pooling of barcoded ONT PCR-cDNA libraries

Quantification, normalisation, and equimolar pooling of individually barcoded Oxford Nanopore PCR-cDNA libraries prior t...

Fragment Analyzer – SS NGS Fragment 1-6000 bp

Standard sensitivity NGS fragment analysis (1-6000 bp range) on the Fragment Analyzer using the DNF-473 kit. Suitable fo...

AMPure XP / SPRI Bead Size Selection

Size selection of DNA or cDNA libraries using AMPure XP or equivalent SPRI beads to enrich for fragments above a target ...

ONT Flow Cell Wash (EXP-WSH004)

Nuclease wash of an Oxford Nanopore flow cell between sequencing runs using the Flow Cell Wash Kit (EXP-WSH004). Removes...

Site Assessment

A thorough observation and documentation of your site's existing conditions before designing. Steps: 1. Walk the s...

Sector Analysis

Map the external energies that flow through your site — sun, wind, water, fire risk, noise, views, wildlife corridors. ...

Zone Planning

Assign elements to permaculture zones (0-5) based on how frequently you need to visit or interact with them. Zones: - Z...

Guild Design

Design a plant guild — a community of mutually beneficial plants that support each other. A guild typically includes: -...

Succession Planning

Plan the sequence of plantings and activities across seasons and years to build soil, establish plants, and develop the ...

COI DNA Barcoding for Consumer Fish Samples

Identifies teleost fish to species via the Folmer COI barcode region using the Ward et al. 2005 primer cocktail. Designe...

Retail tissue collection for mislabeling studies

Standardised collection of retail fish/seafood tissue (sushi, sashimi, fillets) for downstream species-ID. Captures the ...

OpenTaq Cellular Reagent Production (Evaporative Drying)

Produces a functional Taq DNA polymerase reagent without chromatographic purification, following the cellular-reagents a...

Heat-shock Transformation of Chemically Competent E. coli

Standard bench procedure for introducing a plasmid DNA construct into chemically competent E. coli by brief heat-shock. ...

Preparing a Glycerol Stock for Long-term Strain Storage

Cryopreservation method for bacterial strains using glycerol as a cryoprotectant, producing indefinitely-storable frozen...

OD600 Measurement by Spectrophotometer

Quantifying bacterial culture density by measuring optical density at 600 nm — the standard proxy for cell concentration...

Preparing LB Agar Plates with Antibiotic Selection

Producing sterile agar plates with an antibiotic selection marker. The foundational solid-phase culture medium for selec...

Evaporative Drying in a Desiccator Jar (for Cellular Reagents)

Lyophilisation-free method for drying bacterial cell aliquots into room-temperature-stable reagent format, using a seale...

OpenVent Cellular Reagent Production (Evaporative Drying, High-Fidelity PCR)

Produces a functional Vent DNA polymerase (Pyrococcus sp.) reagent as lyophilisation-free cellular reagent, using the sa...

Bst-LF Cellular Reagent Production (LAMP Isothermal Amplification)

Produces a functional Bst polymerase Large Fragment reagent (Bacillus stearothermophilus) as cellular reagent without pu...

RTX Reverse Transcriptase Cellular Reagent Production (One-Enzyme RT-PCR)

Produces a functional RTX reverse transcriptase reagent as cellular reagent without purification. RTX is an engineered p...

Alkaline Lysis Plasmid Miniprep (Birnboim & Doly method)

Classic chemical miniprep for plasmid DNA from small-volume bacterial cultures, using alkaline lysis and differential pr...

Preparing Chemically Competent E. coli by the CaCl2 Method

Standard CaCl2-based preparation of chemically competent E. coli cells, suitable for heat-shock transformation with plas...

SDS-PAGE Gel Preparation and Running (Laemmli discontinuous buffer system)

Denaturing polyacrylamide gel electrophoresis for separating proteins by molecular weight — the foundational protein QC ...

Chelex-100 DNA Extraction for PCR-Ready Template

Fast, low-cost DNA extraction suitable for PCR-based species identification and similar downstream assays. Uses Chelex-1...

Standard PCR Setup and Thermocycling

Foundational Polymerase Chain Reaction procedure for amplifying specific DNA sequences from a template. Covers master-mi...

Agarose Gel Electrophoresis for DNA Visualisation

Standard agarose gel electrophoresis for separating and visualising DNA by size. Uses SYBR Safe (blue-LED transilluminat...

PCR Cleanup by SPRI (Solid-Phase Reversible Immobilisation) Beads

Purification of PCR products (amplicons) using paramagnetic SPRI beads. Removes primers, primer-dimers, dNTPs, salts, an...

Sanger Sequencing Sample Submission (Outsourced)

Preparation and submission of purified PCR products for outsourced Sanger sequencing. Covers concentration measurement, ...

BLAST Species Call and Best-Hit Analysis

Computational procedure for calling species from a Sanger-sequenced barcode read using NCBI BLAST + BOLD Systems. Covers...

LAMP Reaction Setup and Thermal Incubation

Loop-mediated isothermal amplification (LAMP) workflow — uses four to six primers and a strand-displacing Bst polymerase...

LAMP Visual Readout by pH Indicator (Hydroxynaphthol Blue)

Colorimetric readout of LAMP reactions by pH change. LAMP amplification releases protons as the polymerase extends prime...

eDNA Water Filtration for Biodiversity Surveys

Physical filtration of water samples through membrane filters to capture environmental DNA (cellular, extracellular, and...

eDNA Extraction from Filter Membranes (Salt-Precipitation Method)

Salt-precipitation DNA extraction from water-filter membranes preserved in Longmire buffer. Recovers environmental DNA s...

Chelex DNA Extraction for Citizen Submitters (Kitchen Edition)

Kitchen-grade adaptation of lab-standard Chelex-100 DNA extraction (Walsh, Metzger & Higuchi 1991). Designed for cit...

CTAB DNA Extraction (Cross-Tissue Reference Protocol)

High-molecular-weight genomic DNA extraction using cetyltrimethylammonium bromide (CTAB) lysis, chloroform phase separat...

SDS + Salt-Precipitation DNA Extraction (Consumer-Safe Cross-Tissue Protocol)

Genomic DNA extraction using SDS lysis, high-salt protein precipitation, and isopropanol precipitation. No chloroform, n...

Pollen Recovery from Honey (Pre-Extraction Concentration Step)

Pre-extraction step for honey-based DNA work: dissolves a honey sample in warm water, pellets the pollen fraction by low...

Fluorometric dsDNA Quantification (Qubit dsDNA HS Assay)

Fluorometric measurement of double-stranded DNA concentration using the Qubit dsDNA HS (High-Sensitivity) assay. Covers ...