wiki:LEGACY - Collection Protocol amendments for DNA processing

LEGACY - DNA Processing

Tags: CaTissue

BRICCS Study Collection Protocol v1 did not contain any reference to DNA processing. For the initial period of the study, an Access database has been used to record the data. But the data should be held in caTissue.

We need to amend the caTissue procedures to collect the date in future, and also write a script for bulk upload of historic data to the catissue database.

Manual process

1 buffy coat aliquot per participant is stored in the freezer.

Remove the sample - RECORD THAW EVENT DNA extraction - in catissue this is represented as a derived specimen DNA is aliquoted x 5 (1 x 50ul plus 4 x 210ul) Aliquots stored The 4 210ul aliquots are stored in the -20 freezers (5 (aliquots 2 and 3) and 6 (aliquots 4 and 5) ) RECORD FREEZE EVENT Aliquot 1 is stored in a fridge (4 wide, by 3 high by 3 deep) ??? maybe put racks in Aliquot is processed in the nanodrop: produces data for 'A260' 'A280' and 'ng/ul concentration' - these values should apply to all five aliquots, even though they are calculated from one aliquot. Allocate them to the intermediate parent sample and have them propagate. Aliquot is returned to the fridge.


Create new storage type (-20 freezer) 16 racks high x 3 wide - DONE Create new storage type (fridge) - DONE Create new storage type racks for -20 (4 positions deep) - DONE Standard 96 well boxes for DNA 0.5ml 2d barcoded tubes Create new storage locations (freezer5 and freezer 6) (racks) Create new storage locations (fridge) (racks)

Amend protocol to include events and processes as above - DONE

Create a bulk upload process to upload output of Access database

Create an addition to the BRICCS API client to process the above activity, one for the DNA generation, one for the locating of the samples into the freezers.

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Last modified 7 years ago Last modified on 11/29/15 16:52:50
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