QIAGEN RT² Profiler PCR Arrays.

When you add a plate to a batch, upload the RDML file exported directly from your qPCR instrument. Ampliova reads the gene names already embedded in the file and pre-fills the entire 96-well layout automatically.

If your RDML does not contain gene names (e.g. the plate was run without a template loaded in the instrument software), Ampliova will ask for your array catalog number (e.g. PAHS-033Z). It then looks up the exact well→gene mapping from its built-in reference table and fills the layout for you.

In both cases, you only need to assign sample names and biological groups to the experimental wells, typically under 30 seconds.

All QIAGEN RT² Profiler 96-well arrays follow the same structural template. Well assignments for controls and reference genes are identical across all catalog numbers. Only the 84 target gene positions differ by array.

Export the file directly from your instrument software. RDML is preferred (includes amplification curves → efficiency correction). XLS is accepted but will use E = 2.0.

The RT² Profiler 384-well [4×96] format runs 4 samples simultaneously on a single plate using an interleaved layout, not quadrants: each 96-well position maps to a 2×2 block of the 384-well plate, one well per sample.

During the plate wizard, Ampliova detects the 384-well format automatically and asks you to assign a sample name to each of the 4 interleaved samples. The gene mapping is applied identically to all 4 samples.

Ampliova supports two export formats from your instrument:

RDML: the preferred format. Contains raw fluorescence data per cycle, which allows LinRegPCR to compute per-reaction efficiency. The result is efficiency-corrected quantification (Rq = E^−Cq).

XLS / CSV: Ct values only, no amplification curves. Ampliova accepts these files for RT² Profiler plates and automatically uses E = 2.0 for all genes (equivalent to classic ΔΔCq). The gene layout is filled from the catalog number set on the batch. You will see a warning in the analysis settings reminding you that efficiency correction is not available for this plate.

All 96-well and 384-well RT² Profiler arrays are structurally supported (reference gene and control well positions are identical across all arrays). The table below lists arrays whose target gene positions are mapped in the built-in database. Arrays not listed will still work if your RDML contains gene names, or can be identified by entering the catalog number manually at plate import.