Plates

Processing Plate Data

All CE data must be uploaded into MicroSPAT in the "Plate Format". To put FSA files into plate format, zip together all the FSA files from a single capillary electrophoresis run into a single zip file (96 FSA files in a 96 well format run, 384 FSA files in a 384 well format run)

Uploading

To upload the plate, select "choose files" and select the zip. Next select the ladder used on this plate. Press upload and MicroSPAT will process the plate, add it to the database, and calculate the ladder for each well. Multiple Plate zips may be uploaded at once and processed in parallel if they are all selected in the "choose file" prompt. Once complete, the plate(s) will appear in the list below.

Assigning Plate Map

After a plate has been uploaded, a Plate Map may be used to assign each channel to a particular sample for a given locus. A Plate Map is a CSV file containing the assignment of each well to a particular sample and marker. The header will be [Well, locus1, locus2, ...] where [locus1, locus2, ...] are the unique labels of the loci that were run on this plate. Each row then contains the well and the samples contained for each marker. Ex:

Well	L1	L2	L3
A01	P1-Sample1	P1-Sample1	P1-Sample1
...	...	...	...

A demo file showing how a plate where different markers are used in different wells can be found at demo_files/96_well_plate_map.csv. In order to upload a Plate Map, select a plate, and in the right pane press "Choose File" to select the Plate Map CSV. If you are adding new samples, select "Create Samples If They Don't Exist" to add new samples to the database.

Quality Checking

After a plate is selected from the list of uploaded plates, the pane to the right will populate with the plate status. Within the Ladder tab, any wells where the ladder failed are colored as red (failure defined as the sizing quality falls below the ladder SQ Flagging Limit). These may be manually checked and have their ladder peaks called by hand. If there is a systemic issue with ladder peak calling that is better resolved globally, the ladder settings may be changed under the Ladder tab to the left, and the "Recalculate Ladder" button may be pressed to recalculate the ladder across the entire plate.

Manual Ladder Calling

After selecting a failed well, a plot will appear showing the ladder channel, the automatically determined peaks, and the calculated sizing quality for that well. The peaks may be selected and deselected by hand, and the ladder recalculated by clicking "Recalculate Ladder" to the right of the ladder pane.

Locus Performance

After a plate map has been used to assign loci to each well, the wells will be colorized by a rudimentary measure of success. If no signal is detected in a channel for an expected locus base size range, the channel will be colored red. If there is signal, the channel will change to green for optimal signal range, and approach blue as the signal becomes too strong and is potentially beyond the dynamic range of the machine. This view provides a quick measure of plate performance and is useful for identifying plate effects and other potential problems at the experimental level.