Well Plate Templates

Starter layouts for common assays

A blank template becomes useful once controls and replicates are placed deliberately. The layouts below are widely used starting points drawn on the templates above. They are not validated protocols, so adapt them to your assay kit, the relevant CLSI or EUCAST document, or your lab’s SOP. You can rebuild any of them in the plate designer and export a PNG or CSV.

qPCR plate layout on the 96-well template

Each primer pair gets half the plate. Rows A–D hold the target gene and rows E–H the reference (housekeeping) gene, such as GAPDH or ACTB. Every cDNA sample runs as a technical triplicate in three adjacent wells, which leaves room for 14 samples per gene. Running every sample for both genes on the same plate is called a sample-maximisation design, and it keeps run-to-run variation out of the ΔΔCq comparison.

• No-template control (NTC): water instead of cDNA for each primer pair. Amplification here points to reagent contamination or primer-dimers.
• No-RT control: RNA taken through reverse transcription without the enzyme. A signal here means genomic DNA is being amplified.
• Relative quantification: the 2^−ΔΔCq method assumes both assays amplify with similar, near-100% efficiency, so check efficiency with a standard curve first.

The same pattern scales to the 384-well template, where 5–20 µL reactions allow four primer pairs across the same samples. Record Cq thresholds and reaction volumes alongside the map, as the MIQE guidelines recommend.

Broth microdilution (MIC) plate layout

The minimum inhibitory concentration (MIC) is the lowest antimicrobial concentration that prevents visible bacterial growth. In the reference broth microdilution method described in CLSI M07 and ISO 20776-1, columns 1–10 carry a two-fold dilution series in cation-adjusted Mueller–Hinton broth, for example 64 down to 0.125 µg/mL. Rows A–G each take one test isolate at a final inoculum of about 5 × 10⁵ CFU/mL.

• Column 11, growth control: inoculum without antimicrobial. The run is invalid if these wells do not grow.
• Column 12, sterility control: broth only. Any turbidity means the medium was contaminated.
• Row H, QC strain: a reference organism such as Escherichia coli ATCC 25922 or Staphylococcus aureus ATCC 29213, whose MIC must fall in its published range.

Plates are typically read after 16–20 hours at 35 °C. Recording the concentration for each column on the template makes the MIC a direct read-off rather than a calculation.

384-well screening plate with control columns

Primary screens usually test each compound once, so plate quality depends on the controls. Placing a negative and a positive control column on both sides of the plate exposes left-to-right drift from dispensing or reading. With 32 wells of each control, you can calculate the Z′-factor for every plate:

Z′ = 1 − 3(σ_pos + σ_neg) / |μ_pos − μ_neg|

A Z′ of 0.5 or higher indicates an excellent separation between controls. Plates below your cut-off are repeated before hits are called, and confirmed hits then move to dose-response testing for an IC₅₀. Outer rows A and P are the most exposed to evaporation, as covered in common well plate template mistakes.

siRNA knockdown on the 24-well template

Each column is one condition, which keeps pipetting simple and makes the map easy to read at the bench. The mock column separates effects of the transfection reagent from effects of the siRNA. The non-targeting siRNA is the baseline for calculating knockdown. Using two independent siRNA sequences against the same gene helps rule out off-target effects. A positive-control siRNA confirms that transfection worked.

Rows A–C give three wells for RNA extraction and RT-qPCR, typically 24–48 hours after transfection. Row D is kept for a viability or imaging check. Protein knockdown by western blot usually needs 48–72 hours.

Plans for 6-, 12- and 48-well templates

• 6-well, protein or RNA harvest: control cells in A1–A3 and treated cells in B1–B3 give biological triplicates with enough lysate per well for a western blot.
• 12-well, scratch (wound-healing) assay: four conditions in columns 1–4 with three wells each. Mark reference lines on the plate underside so the same fields are imaged at 0 hours and at each later timepoint.
• 48-well, crystal-violet biofilm screen: seven strains in columns 1–7 and broth-only controls in column 8, with six replicate wells per column.

Which template fits your labware?

Many plates look different but share a standard grid. Choose the template by the grid, not by the plastic, well depth or skirt. The table covers the common cases, and the deep-well vs standard 96-well guide explains how those two plates differ in use.

A 1536-well plate is the one standard format without a printable template. Its 32 rows run from A to Z and then AA to AF, across 48 columns at 2.25 mm pitch. At that density, layouts live in software as lists of well IDs rather than on paper. Dishes, flasks and chamber slides do not follow the microplate grid, so a well plate template does not apply to them.

Frequently asked questions