Tag Archives: ABI 7300

Data Analysis – Young Lab ABI 7300 Calibration Checks

All runs (3 runs were conducted) were created using a master mix containing C.gigas gDNA (either 50ng or 100ng), 1X Promega qPCR Master Mix, 0.2uM each of forward/reverse primers (18s; Roberts SR ID: 156, 157). The master mix was mixed well and 10uL were distributed in each well of ABI plates. Plates were sealed with ABI optical adhesive covers.

It should also be noted that this analysis was only done with a single primer set and was not tested on any other qPCR machines. This can easily be done if it is desired, however I think one of the issues still being observed with the machine is sample-independent (see Results section below).

Results:

Here’s an extremely quick and dirty analysis of what these qPCR runs have revealed (across the entire plate, 3 plates of data):

Avg. Range of Cts Across Plates – 1.70

Avg. Std. Deviation of Cts Across Plates – 0.352

Based off of the graphs below (particularly the Ct vs Well Position plot), my conclusion is that the machine reads plates inaccurately in Rows A, B, C, F, G, & H. Rows D & E exhibit the most consistent well-to-well readings and, potentially, could be used for qPCR.

The entire work up (which includes a breakdown of each well position relative to each other) is here (Excel Workbook .xlsx). Below are screen captures of one of the three plates (as an example, since all looked the same) that were used for analysis of the amplification plots, melt curves and Ct vs Well Position and a quick description/assessment of what I have observed.

The amplification plot (below) clearly shows the type of spread in Cts across an entire plate that was observed in each run, as well as a large range in fluorescence detected (Rn) in each well.

The melt curve (below) reflects the large range of detected fluorescence seen in the amplification plot. Additionally, some wells exhibit small “bumps” between 75C and 80C. This provides more evidence for a problem with well-to-well consistency.

A graph of Ct vs. Well Position (below) reveals some enlightening information. From looking at this plot, it’s clear that the machine reads from A1 to A12, then B1 to B12 (reads by row, not column) and so on. This plot reveals that most of the variation seen in Ct values occurs in the two rows closest to the edge of the plate, and within those rows, the middle wells’ Cts are more similar to the Cts observed throughout the rest of the plate.

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qPCR – Test Young Lab qPCR Calibration (Repeat)

This was repeated from earlier today due to the failure of the previous run, but had to use new gDNA since I ran out of the stock I had previously used. Master mix calcs and cycling params are here.

Results:

Amplification in all wells, however well E4 appears to have had some evaporation (and the effects can clearly be seen in the amplification plot below). Still getting ~3 cycle spread across the entire plate, which is disconcerting. Oddly, this is the second day where the 1st run completely failed, but the 2nd run was successful…

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qPCR – Test Young Lab qPCR Calibration (Repeat)

This is a repeat of a run from 20110204. Here’re master mix calcs. This was being repeated to evaluate whether or not the relative differences in Ct values observed on 20110204 are consistent or not across the plate. Cycling params were as follows:

  • 95C – 10min

40 Cycles of:

  • 95C – 15s
  • 55C – 30s
  • 72C – 1m

Melt curve.

Results:

Absolutely no amplification of any kind! Bizarre. Will repeat.

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qPCR – Test Young Lab qPCR Calibration (Repeat)

This is a repeat of an earlier run from today, but with a different qPCR plate. Here’re master mix calcs (bottom half of page). Cycling params were as follows:

  • 95C – 10min

40 Cycles of:

  • 95C – 15s
  • 55C – 30s
  • 72C – 1m

Melt curve.

Results:

All samples amplified and showed a proper dissociation curve. However, it does look like there’s a spread of ~3 Cts across the plate. This is not good, as this is the equivalent of ~10-fold difference in gene expression. Will repeat again and see if specific wells show the same relative differences in Cts.

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qPCR – Test Young Lab qPCR Calibration

Recently, the Young Lab’s ABI 7300 qPCR machine was calibrated. Steven asked me to run a plate and see how well the calibration worked. Ran a plate with C.gigas gDNA and Gigas 18s primers (SR ID: 156 and 157) that are known to amplify gDNA. Master mix calcs are here (top half of page). Cycling params were as follows:

  • 95C – 10min

40 Cycles of:

  • 95C – 15s
  • 55C – 30s
  • 72C – 30s

Melt curve.

Results:

Absolutely no amplification of any kind. However, I did use one of our conventional PCR plates and not one of the ABI “prism” plates. Additionally, when I removed the plate from the machine, the plate looked as though it had been vigorously shaken:

Will repeat this qPCR with a proper ABI “prism” plate.

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