Analyzing the data
About the results screen
The QuantStudio
™
3D Digital PCR Instrument displays a summary
of the imaging data after each successful run. For each
QuantStudio
™
3D Digital PCR 20K Chip imaged, the instrument
displays the following information:
6
1
5
4
7
3
2
1
Chip ID – Displays the ID number of the Digital PCR 20K Chip. If
the instrument cannot read the chip ID, the touchscreen displays
the instrument serial number followed by the time and date of
the run.
2
Time/date stamp – Displays the date and time of the run in
<
yymmdd
>_<
hhmmss
> format.
3
FAM/VIC copy number estimate – Displays the estimated
concentration in copies per µL calculated from the fluorescence
signal associated with the amplification of the nucleic acid
sequence targeted by the FAM
™
and/or VIC
®
dye-labeled probes.
Beside the copy number estimate, the QuantStudio
™
3D
Instrument displays a flag icon, color-coded to indicate the
status of the preliminary analysis of the image data for the
associated probe.
4
Network status icon – Represents the status of the QuantStudio
™
3D Instrument network connection:
•
– Wired (Ethernet) connection selected; connected to
network.
•
– Wired (Ethernet) connection selected; no connection
available.
•
– Wireless connection selected; connected to network.
•
– Wireless connection selected; no connection
available.
5
Data destination icon – Represents the selected data destination:
•
– Cloud destination selected.
•
– USB drive destination selected.
6
File name – Name of the experiment (.eds) file created for the
imaged Digital PCR 20K Chip.
7
Scroll buttons – Allow you to display the results of previously
imaged Digital PCR 20K Chips when running them in a series.
About data quality flags
Data quality flags generated and displayed by the software are a
measure of the overall chip quality, based on well quality
thresholds and other data analysis characteristics.
Note:
For more information on quality assessment in the software,
see the user documentation for the QuantStudio
™
3D
AnalysisSuite
™
Software.
In order, from high quality to low quality:
•
(green) – Review of the analysis results is not required.
This flag is shown if the data meets all quality thresholds.
•
(yellow) – Review of the analysis results is suggested. This
flag is shown if the:
– Instrument cannot clearly identify the population of
unamplified wells.
– Distribution of unamplified wells on the chip is not
uniform.
– Sample concentration is outside the optimal range
(200-2000 copies/µL) for the system as currently defined
by the chip quality metrics.
•
(red) – Review of the analysis results is strongly suggested.
If necessary, reimage the Digital PCR 20K Chip or rerun the
sample. This flag is shown if the total number of filled wells
is < 5000 or the percentage of low quality wells (those with
well quality < 0.5) is > 15%.
Transfer the results
If a data transfer is unsuccessful, you can use the QuantStudio
™
3D
Instrument Run History screen to transfer experiment files to a
USB drive for manual upload to the QuantStudio
™
3D
AnalysisSuite
™
Software. Under normal conditions, the instrument
automatically transfers the results for each imaged chip
immediately following the analysis (to the cloud storage service,
network file server, or USB drive); however, if the network
connection fails or if the USB drive is full, you can transfer the files
manually as follows to make them available for secondary
analysis.
1.
Insert a USB drive into the port on the front of the
QuantStudio
™
3D Instrument.
2.
In the touchscreen, touch in the Main Menu.
3.
In the Settings Menu, touch Run History to view the results
for the past experiments.
4.
In the Run History screen, touch the entry of the experiment
that you want to transfer or view.
5.
In the Results Details screen, touch Export ,then touch Export
again to transfer the file to the USB drive.
6.
When finished, touch several times to return to the Main
Menu, then remove the USB drive from the instrument.
After exporting experiment (.eds) files to the USB drive, you can
upload them to the cloud for analysis using the QuantStudio
™
3D
AnalysisSuite
™
Software.
QuantStudio
™
3D Digital PCR System Quick Reference
9