Opened 5 years ago

Closed 5 years ago

#818 closed enhancement (fixed)

Track volumes of RNAQC aliquots

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v3.7
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

The original quantity assigned to RNA items currently assumes that a single RNAQC aliquot is taken and that the same volume is used for all aliquots. In reality the volumes may be different:

  • If the concentration is low, a larger volume is needed to run Caliper with HiSense setting
  • The Caliper may fail to measure the RNA for various reasons. In this case, a second aliquot is taken and second measurement is made (using the same well).

A number of updates are needed to the wizards:

  • DNA/RNA/FlowThrough registration: The RNA volume is currently set to 51µl, but this need to be increased with 2µl to account for one normal RNAQC aliquot (on Caliper).
  • Create aliquots on Bioanalyzer/Caliper plates: Default RNAQC volumes for normal and HiSense options should be included in the last step. It should be possible for the user to manually change the volumes. The default volumes are 2µl (Caliper normal), 6µl (Caliper HiSense) and 1µl (Bioanalyzer).
  • Import RQS scores from Caliper well table file: This wizard need a way to specify wells that has been re-run and set the extra volume that was used. The extra volume should be recorded as an 'other' event on the RNA item.

Change History (8)

comment:1 Changed 5 years ago by johan

Default RNAQC volumes for normal and HiSense? are 2 µl and 6 µl respectively.

comment:2 Changed 5 years ago by Nicklas Nordborg

Description: modified (diff)
Status: newassigned

comment:3 Changed 5 years ago by Nicklas Nordborg

(In [3545]) References #818: Track volumes of RNAQC aliquots

Changes the default RNA volume in the 'DNA/RNA/FlowThrough registration' wizard to 53 (was 51).

The 'Create aliquots on Bioanalyzer/Caliper? plates' has been updated with input fields for the aliquot volumes. The default values are 2µl for normal, and 6µl for HiSense.

comment:4 Changed 5 years ago by Nicklas Nordborg

Description: modified (diff)

comment:5 Changed 5 years ago by Nicklas Nordborg

(In [3550]) References #818: Track volumes of RNAQC aliquots

Bioanalyzer volume is now set to 1µl and the HiSense option is disabled.

comment:6 Changed 5 years ago by Nicklas Nordborg

(In [3555]) References #818: Track volumes of RNAQC aliquots

The 'Import RQS scores from Caliper well table file' has been updated to make it possible to specify volumes for extra aliquots.

After selecting the Caliper well table CSV file it is possible to select 'Extra aliquots from RNA=Yes'. This will display a plate view of the Caliper plate with active links on wells that have an RNAQC aliquot already. Clicking on a well will open a dialog were the volume and a comment can be specified.

comment:7 Changed 5 years ago by Nicklas Nordborg

(In [3558]) References #818: Track volumes of RNAQC aliquots

Adding files for the popup dialog were the extra aliquot volume is specified (should have been included with [3555]).

comment:8 Changed 5 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed
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