Contents of this Article

Microbial Strains Library
Contents of the Template File

TeselaGen's software allows you to keep track of microbial strains and cell lines as they change and develop.

Microbial Strains Library

However, we need to start somewhere, so let's see how to get data representing our strain database uploaded for the first time. Our example will be a database of fungal microbial strains. If you are originating your database from a well-curated external source, that is great. We can show you how to attach that database directly to your TeselaGen platform via our integration server. For our purposes here, we will simply start with a CSV upload. The upload that we focus on first will be the information listed under:

Materials > Microbial Strains > Upload > Strains

The three-dot button to the right of the upload region can be used to download a template that you can use to upload your strains. Note that you can double-click on these images to see them with better resolution.

Let's take a look at the structure of the strain upload template. Even though the only required fields are NAME and BIOSAFETY_LEVEL, there are several other fields that are interesting to have uploaded en masse so you get it done. Once the prerequisite data has been entered, an upload of a CSV with these columns is straightforward.

Contents of the Template File

Required data
- Name: This is the strain name. You will see it referred to in other CSV upload files as STRAIN_NAME.
- Biosafety level
Optional data
- Alias
- Genus and Species: To associate a strain with a genus and species, the genus and species must first be set in Settings > Genera and Species.
- Genotype: Represents a sub-type of a strain.
- Description
- Plasmid name: This is the plasmid name for a plasmid whose file is specified in the 'GB_FILE' column.
- Genome name: To associate a genome, the genome must already be available in 'Settings > Genomes'.
- Gb File: To associate plasmid files, upload a zip file containing GenBank (.gb or .gbff) or Fasta files along with the CSV. Note: the 'GB_FILE column of the CSV must match the sequence file's name).
- Selection method: To associate a selection method, the selection method must already be set in 'Settings > Selection Methods'.
- Organism class: To associate an organism "class", the name of the group must already be set in 'Settings > Target Organism Class'.
- Growth condition name and description
- Growth medium: Optional. To associate a growth medium, the name of the medium must already be set in 'Materials > Reagents > New Reagent'.
- Temperature
- Shaker speed and throw: if this is specified, you will also need to add the Lenght Unit Code.
- 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. All extended properties are set in 'Settings > Extended Properties' before this upload.

We now have all the reference information about our set of strains in the database. Next, we will want to add information about how the physical samples are stored. In the illustration below, we have filled in the information in the block labeled 'References'.

In the next article, we will show how to get the information about the physical location of the strain database into the system.

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:

Plate Type: Generic 100 Position Tube Box
Tube Type: Eppendorf Tubes 5.0 mL with a screw cap
Fill Rack with Tubes: check
Number of Tubes: 100
Generate Tube Barcodes: uncheck (our upload file has barcodes)
The uploaded file is generated from the Download Template (see the three-dots!)
Assign to Location: Check
Choose Lab: Demo
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, it 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 choose 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.