| Setting Up a Read-Only, Docker-Served JBrowse 2 Instance with Remote Genome Storage via sshfs |
A step-by-step playbook for publishing any reference genome in JBrowse 2 on a Linux server using onl... |
management
|
2025-07-02 |
View
|
| High-Salt CTAB DNA Extraction |
Obtain high-molecular-weight genomic DNA suitable for long-read sequencing or Southern blotting. The... |
sample_prep
|
2025-07-15 |
View
|
| 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 ... |
sample_prep
|
2025-08-04 |
View
|
| Nanodrop analysis of nucleic acid concentration and purity |
This procedure describes the steps for assessing the concentration and purity of nucleic acids (DNA ... |
measurement
|
2025-08-08 |
View
|
| Collection and storage of Helicoverpa armigera for later processing |
A method for collecting Helicoverpa armigera (eggs, larvae, pupae, adults), snap‑freezing whole tiss... |
sample_prep
|
2025-08-09 |
View
|
| Serial Dilution of DNA |
A standardized method for preparing single and serial dilutions of DNA (e.g., 1:10, 1:100, 1:1000) f... |
sample_prep
|
2025-08-11 |
View
|
| 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 usi... |
measurement
|
2025-08-25 |
View
|
| 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 th... |
measurement
|
2025-08-26 |
View
|
| EZ DNA Methylation‑Gold™ Kit — Bisulfite Conversion of DNA |
### Purpose
To convert unmethylated cytosines in DNA to uracil (while preserving 5‑methylcytosine... |
sample_prep
|
2025-08-26 |
View
|
| Agarose Gel Electrophoresis for DNA Integrity/Size Assessment |
## 1. Purpose
To assess DNA integrity, approximate size range, and gross contamination by running... |
measurement
|
2025-08-26 |
View
|
| Bisulfite amplicon sequencing library preparation (using TruSeq adapters) |
A **complete SOP** for generating **MiSeq‑ready bisulfite amplicon libraries** with **TruSeq‑tailed ... |
sample_prep
|
2025-09-03 |
View
|
| 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 Ki... |
sample_prep
|
2025-09-18 |
View
|
| Loading and Running a Flow Cell on a Oxford Nanopore Technologies MinION |
This SOP covers the steps from flow-cell insertion, priming, library loading, starting a sequencing ... |
measurement
|
2025-09-17 |
View
|
| Specimen capture |
The first stage of any molecular phenotyping workflow is to collect the specimen from the environmen... |
sample_prep
|
2025-11-04 |
View
|
| 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. |
sample_prep
|
2025-11-04 |
View
|
| 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. |
sample_prep
|
2025-11-04 |
View
|
| 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 ... |
sample_prep
|
2025-11-04 |
View
|
| Culture of Helicoverpa armigera |
This protocol outlines the procedures for maintaining and breeding Helicoverpa armigera in a laborat... |
sample_prep
|
2025-11-04 |
View
|
| Direct cDNA sequencing V14 with SQK-LSK114 |
This protocol describes how to carry out sequencing of cDNA using a reverse transcription and strand... |
sample_prep
|
2025-11-04 |
View
|
| Collecting and Transporting *Helicoverpa* Samples Between Laboratories |
Collection at a collaborating lab and transport to the home lab of any *Helicoverpa* life stage (egg... |
sample_prep
|
2025-11-06 |
View
|
| Transfer of tissue samples between sites in Australia for downstream genomics studies. |
Ensure lawful, safe, and traceable transfer of tissue samples between Australian sites for genomics ... |
sample_prep
|
2025-11-07 |
View
|
| 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 colum... |
sample_prep
|
2025-11-07 |
View
|
| Fragment Analyzer – RNA (Eukaryotic) |
Run total RNA on the Fragment Analyzer using the eukaryotic RNA analysis mode. |
measurement
|
2025-11-07 |
View
|
| 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... |
sample_prep
|
2025-11-07 |
View
|
| Fragment Analyzer – HS Large Fragment 50Kb |
|
measurement
|
2025-11-07 |
View
|
| PacBio Iso‑Seq Library Preparation — SMRTBell Ligation |
SMRTbell Express Template Prep v2.0 with adapter‑ligation barcodes (ALB) |
sample_prep
|
2025-11-07 |
View
|
| PacBio Sequel II — Polymerase Binding and Optional Post‑Binding Pooling |
Bind Sequel II polymerase to finished SMRTbell Iso‑Seq libraries, optionally pool after binding prio... |
sample_prep
|
2025-11-07 |
View
|
| DEMO: DNA Extraction Protocol |
Demonstration procedure for genomic DNA extraction from tissue samples. |
sample_prep
|
2025-12-27 |
View
|
| DEMO: DNA Extraction Protocol |
Demonstration procedure for genomic DNA extraction from tissue samples. |
sample_prep
|
2025-12-27 |
View
|
| DEMO: ONT Library Preparation |
Demonstration procedure for Oxford Nanopore library preparation. |
sample_prep
|
2025-12-27 |
View
|
| DEMO: MinION Sequencing Run |
Demonstration procedure for Oxford Nanopore MinION sequencing. |
measurement
|
2025-12-27 |
View
|
| DEMO: Dorado Basecalling Pipeline |
Demonstration procedure for ONT basecalling using Dorado. |
data_transformation
|
2025-12-27 |
View
|
| DEMO: Minimap2 Read Alignment |
Demonstration procedure for aligning ONT reads with Minimap2. |
data_transformation
|
2025-12-27 |
View
|
| DEMO: Clair3 Variant Calling |
Demonstration procedure for variant calling using Clair3. |
data_transformation
|
2025-12-27 |
View
|
