Note: double click on any image for a higher resolution view.

Now that we have the reference information for our archive uploaded to:

Materials > Microbial Strains

We can view that information as shown:

It is time to specify where the actual samples sit. The key upload will be via

'Inventory > Plates'. I know, strange. Because we are using 100 slot indexed boxes we need to use 'plates' since those entities are indexed. Go to:

Inventory > Plates > Upload > Microbial Plate CSV

Let's look carefully at our options and from the Plate Type dropdown menu choose:

  1. Plate Type: Generic 100 Position Tube Box

  2. Tube Type: Eppendorf Tubes 5.0 mL with screw cap

  3. Fill Rack with Tubes: check

  4. Number of Tubes: 100

  5. Generate Tube Barcodes: uncheck (our upload file has barcodes)

  6. The uploaded file: generated from the Download Template (see the three-dots!)

  7. Assign to Location: check

  8. Choose Lab: Demo

  9. Tags: Demo

The uploaded CSV file will have the following data represented:

PLATE_NAME

Required. This will be the name of the box if you are uploading a box of tubes.

PLATE_BARCODE

This will be the box barcode if uploading a box of tubes.

TUBE_BARCODE

This is the individual tube barcode.

WELL_LOCATION

For example, this is the letter-number index of a microtiter plate (A1, A2,...) or the numeric index of a box (1, 2, 3...).

SAMPLE_NAME

Optional. If provided, will override the auto-generated sample name.

STRAIN_NAME

Required. This will link the uploaded data to the strain information, and create requisite links between material-sample-aliquot.

PLASMID_NAME

Conditional. The plasmid name is required if the strain is transgenic.

GB_FILE

Conditional. The Genbank file is required if the strain is transgenic.

REAGENT_NAME

Optional. If used, the reagent name must have already been uploaded via 'Materials > Reagents'.

REAGENT_LOT_NAME

Optional. If used, the reagent lot name must have already been uploaded via 'Inventory > Reagent Lots'.

REAGENT_VOLUME

Optional. If used, the reagent volumetric unit must also be specified.

REAGENT_VOLUMETRIC_UNIT

Optional. Required if reagent volume is specified.

REAGENT_CONCENTRATION

Optional. If used, the reagent concentration unit must also be specified.

REAGENT_CONCENTRATION_UNIT

Optional. Required if reagent concentration is specified.

TOTAL_VOLUME

Optional. If used, the total volumetric unit must also be specified.

TOTAL_VOLUMETRIC_UNIT

Optional. Required if the total volume is specified.

MASS

Optional. If used, the mass unit must also be specified.

MASS_UNIT

Optional. Required if the mass is specified.

ext-plate-

This upload accepts extended properties for the plates. Add a property name to this header (ex. 'ext-plate-Date of Purchase') and values to the rows. To add additional plate properties just duplicate the column header.

ext-tube-

This upload accepts extended properties for the tubes. Add a property name to this header (ex. 'ext-tube-Date of Purchase') and values to the rows. To add additional tube properties just duplicate the column header.

ext-strain-

This upload accepts extended properties for the strains. Add a property name to this header (ex. 'ext-strain-Date of Purchase') and values to the rows. To add additional strain properties just duplicate the column header.

ext-sequence-

This upload accepts extended properties for the sequences. Add a property name to this header (ex. 'ext-sequence-Date of Purchase') and values to the rows. To add additional sequence properties just duplicate the column header.

ext-aliquot-

This upload accepts extended properties for the aliquots. Add a property name to this header (ex. 'ext-aliquot-Date of Purchase') and values to the rows. To add additional aliquot properties just duplicate the column header.

ext-sample-

This upload accepts extended properties for the samples. Add a property name to this header (ex. 'ext-sample-Date of Purchase') and values to the rows. To add additional sample properties just duplicate the column header.

Only 'PLATE_NAME' and 'STRAIN_NAME' are strictly required. However, it is well worth the time to gather all the data you wish to associate with the strains and pull them together for the upload. Note also that you can always delete an upload and try again very easily by going to 'Data > Import Collections', finding the import, and deleting it.

If we chose to place the upload in a location, we will be prompted... in this case we choose to place the boxes manually in the freezer:

Let's choose the -80C Freezer No. 2:

And let's put our boxes in Shelf 2, Rack 2...

After uploading our multi-position boxes (defined as "plates"!) are listed:

Double click on one of the records to see the detailed record view of the box and it's contents:

Note: A known issue is that the use of the word 'plate' for a multi-indexed box can be a source of confusion. This will be adjusted to conform with more common usage ;)

At this point, we have filled out all the boxes in our little hierarchy and our data is safe, well organized, and connected.

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