#425 closed task (fixed)
Generate a lab protocol for RNA -> cDNA processing
Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
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Priority: | major | Milestone: | Reggie v2.12 |
Component: | net.sf.basedb.reggie | Keywords: | |
Cc: |
Description
This is part of the RNA->cDNA processing group of wizards (see #422).
The protocol is needed before the actual lab work is started. The RNA selection wizard (#424) has created a child bioplate with the next set of RNA items to be processed.
This wizard should generate a list with the following information:
- Fields for date, operator, comments, etc.
- RNA name and storage location
- Work plate location
- Quantities to use (depends on QC)
- .... more?
Change History (24)
comment:1 by , 12 years ago
Status: | new → assigned |
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comment:2 by , 12 years ago
comment:3 by , 12 years ago
comment:4 by , 12 years ago
comment:5 by , 12 years ago
comment:6 by , 12 years ago
(In [1793]) References #425: Generate a lab protocol for RNA -> cDNA processing
Include empty wells in the list protocol. Added some notes about print settings for list vs. plate layout. Restrict width of screen layout to better see how the printed version will look (also fixed on the Histology and Allprep protocols).
comment:7 by , 12 years ago
(In [1794]) References #425: Generate a lab protocol for RNA -> cDNA processing
Added an optional field to enter the current Stratagene concentration. If it is used, the wizard will automatically calculate volumes to use as for the regular RNA items. If not used, the wizard will add a remark about how much RNA to use (eg 1.1 or 1.22 depending on QC).
comment:8 by , 12 years ago
comment:9 by , 12 years ago
comment:10 by , 12 years ago
comment:11 by , 12 years ago
(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.
comment:12 by , 12 years ago
comment:13 by , 12 years ago
comment:14 by , 12 years ago
comment:15 by , 12 years ago
Milestone: | Reggie v2.x → Reggie v2.12 |
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comment:16 by , 12 years ago
comment:17 by , 12 years ago
Resolution: | → fixed |
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Status: | assigned → closed |
comment:18 by , 12 years ago
(In [1898]) References #425: Generate a lab protocol for RNA -> cDNA processing
Added possibility to register an 'externalId' and 'NDConc' annotation on external mRNA items which will then be used in the lab protocols. The registration has to be done using the regular BASE interface after the mRNA plate has been created.
IMPORTANT! Do not change the 'name' on external items since then they will not be recognized as external anymore.
comment:19 by , 11 years ago
comment:20 by , 11 years ago
(In [1919]) References #425: Generate a lab protocol for RNA -> cDNA processing
- Changed order of columns in the list protocol.
- Use white background in the plate layout.
- Amount of water is right-aligned in each cell.
- Samples with no storage box (eg. stratagene) now have an empty line so that volumes are aligned vertically.
- Latest stratagene concentration is stored and re-used the next time.
(In [1745]) References #425: Generate a lab protocol for RNA -> cDNA processing
Two variants of the protocol can be created. One with a list layout and aone with a plate layout.