Opened 8 years ago

Closed 8 years ago

#875 closed enhancement (fixed)

Soft and hard target amount for NeoPrep

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.3
Component: net.sf.basedb.reggie Keywords:

Description (last modified by Nicklas Nordborg)

The NeoPrep has a rather wide working range (25-100 ng) of input RNA. We have currently optimized our wizards for the higher amount.

While this works fine for the majority of cases there are a few that it doesn't work for:

  1. We get a negative dilution volume if the remaining quantity of the RNA is higher than the target amount but the concentration is too low (<8ng/µl since we set target amount to 120ng) so we don't reach this when only taking 15µl.
  2. We get NotEnoughRemainingQuanity flag when the remaining quantity is lower than the target amount.

Both cases should be solved by calculating how much RNA we get if we take 15µl. If this is higher than the lower input limit accepted by the NeoPrep we should include the RNA and not flag it and set the volume of water to 0.

The currently specified amount that is set as the RNATargetAmount on pre-normalization protocols is the 'soft' target amount. We need a new annotation for setting the 'hard' target amount.

This change affects several wizards:

  • The pre-normalization wizard
  • The library preparation design wizards
  • The lab protocols for NeoPrep library preparation

Change History (7)

comment:1 by Nicklas Nordborg, 8 years ago

Description: modified (diff)

comment:2 by Nicklas Nordborg, 8 years ago

Status: newassigned

comment:3 by Nicklas Nordborg, 8 years ago

(In [3829]) References #875: Soft and hard target amount for NeoPrep

Added RNAMinimalAmount annotation type.

comment:4 by Nicklas Nordborg, 8 years ago

(In [3831]) References #875: Soft and hard target amount for NeoPrep

The "RNA concentration normalization" wizard has been updated with support for the RNAMinimalAmount annotation. If the annotation is not set the minimal amount is assumed to be the same as the RNATargetAmount.

comment:5 by Nicklas Nordborg, 8 years ago

(In [3832]) References #875: Soft and hard target amount for NeoPrep

The "Library preparation design" wizards have been updated.

The "Amount of RNA" input field has been replaced with a protocol selection list and the amount and volumes are taken from the RNATargetAmount, RNAMinimalAmount and RNATargetVolume annotations.

The initial selected protocol is selected based on the RNATargetAmount (0.15 for NeoPrep and 0.50 for manual). There is currently no way to only use the project default setting to select a protocol since there are two variants of the wizard.

The "Auto-select" function is now based on the selected protocol instead of the amount.

A new annotation type DilutionVolume has been created and is used to store the target volume when diluting the RNA. This is used by the lab protocols to get rid of the hard-coded volumes.

The "Auto-design" is still using hard-coded volumes. This need to be fixed.

comment:6 by Nicklas Nordborg, 8 years ago

(In [3833]) References #875: Soft and hard target amount for NeoPrep

Added LibPrepTarget target annotation. This MUST be set on normalization protocols to specify if they are for Manual or NeoPrep.

This makes it possible to get rid of all almost all hard-coded target volumes/amounts in the other wizards. The "Auto-select" and "Auto-design" functions have been updated to only use the information from the protocols.

NOTE! When updating to this Reggie version it is recommended that there are no mRNA/Library plates in progress, since it is not certain that the calculations when printing lab protocols will be correct if the mRNA/Library plate was created with the old Reggie version.

comment:7 by Nicklas Nordborg, 8 years ago

Resolution: fixed
Status: assignedclosed
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