Select RNA items for library preparation

[Nicklas Nordborg]

This is the first step in the RNA->cDNA processing group of wizards (see #422).

The goal of the wizard is to select a number of RNA items for the next round of processing. There are a lot of "rules" for the selection and the wizard need to be able to mix manual selection with automatic suggestions.

The basic schema is to use an 8x8 portion of a 8x12 plate (rows A-H, columns 3-10). This gives us 64 positions, but some should be used with Stratagene (~4) and some RNA items (~4) should be replicated in two positions.

The placement of Stratagene and replicates need to consider downstream pooling and barcoding schemes so that the desired spread is achieved.

Columns 1, 2, 11 and 12 can be used to manually add extra RNA items.

A subset of the items need to be selected/suggested for quality control. This affects the quantity that should be taken from the RNA items.

The wizard is completed by creating a new bioplate with child items (mRNA). The creation dates are left empty to indicate that the plate has not yet been processed.

[Nicklas Nordborg]

(In [1742]) References #424: Select RNA items for library preparation

It should now be possible to use this wizard for creating a plate with mRNA items. There are currently two main options for selecting RNA:

• Manually using the regular BASE list interface. Unfortunately, it is not possible to filter away RNA that already has mRNA child items.

• File import using a tab-separated file. The file should have 3 or four columns: name of RNA, work plate row (A-H), work plate column (1-12), optional QC flag

The automatic RNA selection remains to be implemented.

A lot of error checking, etc. has been implemented. Eg. checking for enough remaining quantity, etc. but may it may have to be fine-tuned.

There is also still some code cleanup to be done, but this can probably be made more efficiently when some of the other wizards are in place since there may be some common patterns.

Before the wizard can be used a RNA extract item with the name 'Stratagene' must be created by hand. This will be done by the installation wizard in the future. NOTE! This item can interfere with the RNAQC wizards so they must also be checked/fixed!

[Nicklas Nordborg]

(In [1760]) References #424: Select RNA items for library preparation

Implemented a simple auto-selection feature that find:

• RNA items with no child mRNA
• A non-empty creation date
• Remaining quantity >= 1.1µg
• Not manually included on the mRNA plate
• Sorted by RNA plate and location: plate, row, column

The user designing the plate need to account for replicates/stratagene by leaving room on each pool and then using copy/paste to duplicate some RNA. The user must also manually assign items for QC.

[Nicklas Nordborg]

(In [1761]) References #424: Select RNA items for library preparation

Added a 'special select' menu that can be used to quickly select wells with a certain condition. For example, all empty wells, wells with Stratagene, wells with an error, etc.

[Nicklas Nordborg]

(In [1769]) References #424: Select RNA items for library preparation

Added filter that exclude RNA with mRNA child items to the 'Manual select' dialog. This depends on the bug fix ​http://base.thep.lu.se/ticket/1736 so we now require BASE 3.2.1 for Reggie.

[Nicklas Nordborg]

(In [1770]) References #424: Select RNA items for library preparation

Fixed problems with variable names/types in the auto-select wizard.

[Nicklas Nordborg]

(In [1789]) References #422, #424 and #425. Renamed 'Stratagene' to 'Stratagene.r' to follow the general naming convention for RNA items.

[Nicklas Nordborg]

(In [1790]) References #424: Select RNA items for library preparation

Added a 'switch' button that can be used when two wells are selected to switch the RNA between them.

[Nicklas Nordborg]

(In [1791]) References #424: Select RNA items for library preparation

The 'special select' popup menu is now triggered by mouse click instead which should make it easier to use if the mouse slips just a little bit outside the toggle icon (before it was automatically hidden).

Also added a 'None' option which always deselect all wells (eg. no toggle as the other options do).

[Nicklas Nordborg]

(In [1792]) References #424, #425 and #436. Added a 'comments' field on the mRNA plate design wizard. The comment is included in the lab protocol and in the final mRNA registration wizard.

[Nicklas Nordborg]

(In [1795]) References #424 and #425. Do not use 'pool' in the wizards/lab protocols since that may be confusing. Pools are not created until later.

[Nicklas Nordborg]

(In [1796]) References #424: Select RNA items for library preparation

Added a context-menu popup with cut/copy/paste and a few other options to right or middle mouse button (depending on user setting).

[Nicklas Nordborg]

(In [1800]) References #424 and #425. Added support for marking wells as used by an 'External' RNA item not tracked by BASE. This will be indicated in the lab protocols, but information about concentration and volumes to use must be picked from another source.

[Nicklas Nordborg]

(In [1802]) References #424 and #425. Changed plate design to use 5 pools of 16 on each plate. This leaves just 1 column on each side free for extra biomaterial.

[Nicklas Nordborg]

(In [1803]) References #424: Select RNA items for library preparation

Changed the auto-select functionality to use a popup with options to set the filter criteria (eg. minial remaining quantity). RNA that doesn't match the filter can be 'flagged' with an annotation (DisableAutoProcessing) and saved to a specific 'Flagged RNA' biomaterial list.

• The DisableAutoProcessing annotation is a string containing the reason that the RNA can't be used to create mRNA.
• The 'Flagged RNA' list is intended for another (to be defined) wizard that should allow the administrator to decide if more lysate whould be processed or if the backup piece should be used (if possible).

[Nicklas Nordborg]

(In [1807]) References #424 and #425. Added support for selecting different pooling layouts. It should be relatively easy to add more layouts in the future. Most of the functionality is in the 'pools.js' file which define the available layouts using some properties and some customization methods. The selected layout is stored as an annotation PoolSchema on the mRNA bioplate. The annotation is then copied to the cDNA plate when that is created. The layout is also used in the plate-view lab protocol.

The barcode layout wizard (#456) will use the selected pool schema as a starting point, but it should also be possible to change and select variants so that all barcodes are used evenly.

[Nicklas Nordborg]

(In [1809]) References #424, #425 and #456. Restructure the plate-handling javascript so that it is easier to re-use on different pages.

The barcode wizard now display the intended barcodes, but it is still only visual and there is not yet possible to change or save the information.

[Nicklas Nordborg]

(In [1816]) References #424: Select RNA items for library preparation

Added support for setting comments per well.

[Nicklas Nordborg]

(In [1819]) References #424: Select RNA items for library preparation

Some minor changes to background color mappings for errors, warnings and selected wells. Also removed a debug line that added a comment whenever the 'Toggle QC' button was used.

[Nicklas Nordborg]

(In [1881]) References #424: Select RNA items for library preparation

Update "Flagged RNA" information if a flagged RNA is manually selected. Make it possible to select a flagged RNA directly in the popup dialog.

[Nicklas Nordborg]

(In [1889]) References #436 and #424.

Added support for registering a mRNA plate as failed. No child cDNA plate is created and the parent RNA are placed in the "Flagged RNA" biomaterial list and annotated with Flag=mRnaPlateFailed. This annotation is now also used by the auto-select RNA wizard to flag RNA with not enough remaining quantity (Flag=NotEnoughRemainingQuantity).

Changed the DisableAutoProcessing annotation to AutoProcessing and it is now also an enumeration (Disable, ReProcess). Items without no value for the AutoProcessing annotation should follow the regular workflow. Other values may be used by wizards to trigger special actions. The Create new mRNA plate wizard has support for the AutoProcessing=ReProcess which should be used for RNA that has been processed once already. The ReProcess annotation override all filter checkes usually done by the auto-select function.

Handling RNA that is flagged is part of ticket #455 and is not sheduled until some later release.

[Nicklas Nordborg]

Closing this ticket for now. There may be some smaller issues to be fixed., but hopefully no major ones.

[Nicklas Nordborg]

(In [1928]) References #424: Select RNA items for library preparation

Display 'loading...' animations when loading information about auto-selected RNA or RNA from a file.

[Nicklas Nordborg]

(In [1929]) References #424, #425, #457, #479. Re-designed protocols to make the header section a bit more compact when the comment text is large. Display a warning when the remaining RNA quanitity is below 1.5 times the required amount (eg. 1.1µg or 1.22µg).

[Nicklas Nordborg]

(In [1938]) References #424: Select RNA items for library preparation

Add support for selecting 'Stratagene' when designing a new mRNA plate.

[Nicklas Nordborg]

(In [1939]) References #424: Select RNA items for library preparation

Added RQS/RIN values to the display. A warning is displayed for scores below 8. This is currently hard-coded, but will be user selectable in the future.

[Nicklas Nordborg]

(In [1940]) References #424: Select RNA items for library preparation

Added filter for RIN/RQS ≥ 6 in the auto-select wizard. RNA below this value are flagged with LowQualityScore annotation and place in the 'Flagged RNA' list.

[Nicklas Nordborg]

(In [1941]) References #424: Select RNA items for library preparation

Fixed a NullPointerException when selecting Stratagene, which doesn't have RNAQC child items.

[Nicklas Nordborg]

(In [1942]) References #424: Select RNA items for library preparation

Added support for setting the RNA quantities to use for regular processing and for QC. Default values are 1.1 and 1.22 µg as before. The auto-select wizard uses the lower quantity when searching for RNA.

[Nicklas Nordborg]

(In [1943]) References #424: Select RNA items for library preparation

Adding LowQualityScore as a valid value for the Flag annotation.

[Nicklas Nordborg]

(In [1945]) References #424: Select RNA items for library preparation

Added options to set remaining quantity and RQS/RIN levels in auto-select RNA wizard.

[Nicklas Nordborg]

(In [1946]) References #424: Select RNA items for library preparation

Added support for manually flagging an RNA item.

[Nicklas Nordborg]

(In [1947]) References #424: Select RNA items for library preparation

Add support for custom warning levels for remaining quantity and RQS/RIN scores.

Do not manually flag items if clicking 'Cancel' in the dialog

Add option to not flag RNA that has been automatically flagged.

[Nicklas Nordborg]

(In [1949]) References #424: Select RNA items for library preparation

Fixed an issue with flagged RNA not being added to the "Flagged RNA" list.

[Nicklas Nordborg]

(In [1951]) References #424: Select RNA items for library preparation

Add link to "Case summary" in the context menu in the "Select RNA" wizard and in the "Flagged RNA" dialog.

Add support for showing the "Case summary" as a popup window.

[Nicklas Nordborg]

(In [1960]) References #424: Select RNA items for library preparation

Minor changes to make empty and copied wells easier to see in the GUI.