Once you begin running bird sexing PCR workflows regularly, consumables and reagent planning become an important part of maintaining efficient workflows.
This guide covers:
- common consumables
- scaling workflows
- replenishing starter kits
- planning for larger sample numbers
- purchasing reagents separately
Understanding workflow consumables
Bird sexing PCR workflows typically involve consumables for:
- DNA extraction
- PCR amplification
- gel electrophoresis
- sample handling and organisation
Unlike core equipment, these items need periodic replenishment depending on workflow frequency and sample throughput.
What are the essential reagents and consumables?
The following reagents and consumables are all used in the bird sexing workflow, and can be found in the Bird Sexing Bundle in quantities sufficient for sexing 48 birds (with some reagents left afterwards).
Once you have used them up you can buy them as individual items from our store.
| DNA Amplification | Description | Amount used per PCR |
|---|---|---|
| 5x HOT FIREPol Master Mix | 5× concentrate of the PCR reaction mix, lacking bird sexing primers, water, and the template DNA. | 4 µL per 20 µL PCR |
| PCR grade water | Extremely pure water with no contaminants. | 12 µL per 20 µL PCR |
| Bird sexing primers | DNA “tags” defining the region to be amplified. Learn how to decide which primers are suitable for your bird species. | 2 µL per 20 µL PCR |
| DNA Extraction | Description | Amount used per extraction |
|---|---|---|
| HotSHOT DNA Extraction Kit | An inexpensive, easy-to-use DNA extraction method. Learn how to use it for feathers or blood spots. | 75 µL of extraction solution and 75 µL neutralising buffer |
| Agarose gel electrophoresis | Description | Amount used per gel* |
|---|---|---|
| 10x TBE buffer (diluted to 0.5× before use) | A buffered solution used for casting and running agarose gels. Bought as a 10× stock solution, it is diluted ×20 to make a 0.5× TBE buffer. | 0.5× TBE: 25-50 mL per gel, and 40-50 mL running buffer |
| Agarose tablets | A concentrated agarose tablet that is dissolved in 0.5x TBE buffer to form an agarose gel | 1× 0.5g tablet per 25 mL gel, or 2× 0.5 g tablets per 50 mL gel |
| GelGreen DNA stain (or other blue-light compatible stain) | A dye that fluoresces green when bound to DNA and exposed to blue light | 2.5 µL per 25 mL gel, or 5 µL per 50 mL gel |
| 100 bp DNA ladder | A mixture of different-sized DNA fragments in 100 bp increments, used to determine the size of the DNA fragments you are studying, in comparison | 5 µL per lane (use two per gel row at either end, or one in the middle of the gel) |
*8 samples or 18 samples with the Add-a-lane comb
| Plastics | Description | Amount used per batch of 8 samples, plus 2 controls |
|---|---|---|
| PCR tubes | 0.2 mL tubes used for HotSHOT DNA Extractions and PCR | 20-30 PCR tubes |
| 1.5 ml tubes | 1.5 mL tubes for making batch PCR mixes | One tube per batch PCR mix |
| 2-200 µL pipette tips | Pipette tips used for all pipetting steps with both pipettes | ~28 tips without a DNA extraction dilution step, and ~38 tips with a dilution step. |
Scaling beyond beginner workflows
As workflows expand, users often begin planning for larger sample batches, repeated weekly workflows, teaching and workshop use or multiple operators.
At this stage, users may choose to purchase consumables in larger quantities, standardize workflow layouts, separate pre-PCR and post-PCR work areas, and maintain dedicated storage for reagents and plastics.
Here’s a guide to topping up the bird sexing bundle for larger numbers of samples.
Please note that these calculations are based on running eight samples plus two controls plus two DNA ladder lanes in a single batch, i.e. a single row gel. If you are using the Add-a-Lane comb, you can run more samples per gel and therefore use fewer reagents for agarose gel electrophoresis per sample.
| Item | 100 birds | 200 birds | 400 birds |
|---|---|---|---|
| HotSHOT DNA Extraction Kit | N/A | N/A | N/A |
| 5x HOT FIREPol Master Mix | 1 × 400 µL tube | 1 × 1000 µL tube | 2 × 1000 µL tubes |
| PCR grade water | 1 × 5 mL bottle | 2 × 5 mL bottles | 3 × 5 mL bottles |
| Bird sexing primers | N/A | 1 × 400 µL tube | 2 × 400 µL tubes |
| 10x TBE buffer | 1 × 50 mL tube | 2 × 50 mL tubes | 4 × 50 mL tubes |
| Agarose tablets | 1 × 10 tablets | 3 × 10 tablets | 8 × 10 tablets |
| GelGreen DNA stain | N/A | 1 × 100 µL tube | 1 × 200 µL tube |
| 100 bp DNA ladder | N/A | 1 × 200 µL tube | 2 × 200 µL tubes |
| PCR tubes | 2 × 100 tubes | 1 × 500 tubes | 1 × 1000 tubes, and 1 x 100 tubes |
| 1.5 ml tubes | N/A | N/A | N/A |
| 2-200 µL pipette tips | 2 × boxes of 96 tips | 7 × boxes of 96 tips | 17 × boxes of 96 tips |
Buying reagents and consumables separately
As workflows become more established, many users begin sourcing individual consumables separately depending on available stock, workflow preferences, regional availability, throughput, and storage considerations.
If you are restocking reagents or already have pipettes and the other equipment in the Bird Sexing Bundle, you can use the table below to work out what you need for a given number of samples.
| Item | 100 birds | 200 birds | 400 birds |
|---|---|---|---|
| HotSHOT DNA Extraction Kit | 1 × HotSHOT DNA Extraction Kit | 1 × HotSHOT DNA Extraction Kit | 1 × HotSHOT DNA Extraction Kit |
| 5x HOT FIREPol Master Mix | 1 × 1000 µL tube | 1 x 1000 µL tube, and 2 x 100 µL tubes | 2 × 1000 µL tubes, and 1 × 400 µL tube |
| PCR grade water | 1 × 5 mL bottle | 2 × 5 mL bottles | 3 × 5 mL bottles |
| Bird sexing primers | 1 × 400 µL tube | 2 × 400 µL tubes | 3 × 400 µL tubes |
| 10x TBE buffer | 2 × 50 mL tubes | 3 × 50 mL tubes | 5 × 50 mL tubes |
| Agarose tablets | 3 × 10 tablets | 5 × 10 tablets | 10 × 10 tablets |
| GelGreen DNA stain | 1 × 100 µL tube | 1 × 200 µL tube | 1 × 200 µL tube, and 1 × 100 µL tube |
| 100 bp DNA ladder | 1 x 200 µL tube | 1 × 500 µL tube | 1 × 500 µL tube |
| PCR tubes | 1 x 500 tubes | 1 × 1000 tubes | 1 x 1000 tubes, and 1x 500 tubes |
| 1.5 ml tubes | 1 x 100 tubes | 1 x 100 tubes | 1 x 100 tubes |
| 2-200 µL pipette tips | 5 × boxes of 96 tips | 10 × boxes of 96 tips | 20 × boxes of 96 tips |
Top Tip: Workflow organization matters
As workflows scale, operational organization becomes increasingly important.
Good practices include:
- careful sample labelling
- maintaining clean work areas
- using controls
- organising consumables before starting workflows
- tracking reagent use over time
Many users find that simple workflow checklists and sample tracking sheets become increasingly useful as sample numbers increase.
Plan your workflow using our cost calculator worksheet.
Access the cost calculator
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