DArT sample file format description and preparation method

DArT sample tracking file is used to define and track samples, once the plate(s) arrives into our facility. Technically this is a “comma separated values” (*.csv) file with the following columns:

PlateID,Row,Column,Organism,Species,Genotype,Tissue,Comments

The easiest way to create this file is to use the function Create template file outlined below in Steps to Create a Sample Tracking File. After you create a template, fill the Genotype column – this will usually be enough to create an appropriate sample tracking file to order the service.

Please refer to the guidelines below and examples as a check list before submitting the file.

Please note that Genotype Name can be any string of less than 100 characters long, uniquely identifying the sample. Please, observe the character restrictions mentioned below.

Sample Tracking File Guidelines

Requirement Description
Commas (,) Commas (,) must only be used to separate fields in the file. Do not use them inside any field (e.g. as a part of genotype name).
Illegal Characters Other characters which cannot be used are: semi colon (;), single quote (‘) and double quote (“).
Mandatory fields All fields must have values except for Species and Comments, which may remain blank.
Species Name If there is any uncertainty with the Species Name, leave the Species Name column blank or place the Species Name in the Comments column and leave the Species Name column blank.
94 Sample Plates As we operate on 94 sample per plate basis, file cannot not contain information for wells G12 and H12.
Empty wells Only informative records should be left in the file. We WILL NOT ACCEPT files with records not representing legitimate samples, as for example BLANK, NA, WATER, TBA, ‘-‘ etc.
Name Compliance Names of organisms and tissues have to comply with our requirements. Using the ‘Create template file’ function will assist in you in finding required values. If you can’t find entry you require, please contact us.
Name Length Names of genotypes can be any string of less than 100 characters, unambiguously identifying the sample, observing the character restrictions mentioned above.
Unique Combinations Each combination of PlateID, Row and Column has to be unique within the sample tracking file.

Filling Partial Plates Guidelines

If you have less than 94 samples or number of your samples is not an exact multiplication of 94 and the last plate is partially filled, please observe the following guidelines:

  • Organize your samples COLUMN-WISE starting from the well A1 and continuing B1, C1 etc. Once column 1 has been filled to H1, the next sample will go to A2, B2 etc. Any well(s) left without assigned sample MUST BE deleted from the sample tracking file. Please, see picture below that illustrates correct organization of the samples in partial plate and comparison to fully filled plate.
  • Make sure you comply with requirement Empty wells outlined above related to creation of the sample tracking file .
Partial plate arrangement (example only)
arrows show order of loading
Full plate
notice G12 and H12 left empty

*green circle represents a well filled with the sample, white circle represents an empty well

Steps to Create a Sample Tracking File

Step Action Comments
1. Select Download the Sample Tracking File Template button to save the file on your system.
2. Prepare the downloaded CSV file by adding your data: Sample identifier into the Genotype column and optionally any note/comment into the Comment column. Refer to the Requirement Table and examples to assist with populating the data file which will help avoid validation errors on upload.
3. When ready to order, go to the New Order page. You may need to log back into Online Ordering.
4. Select the Product and add a Comment if required.
5. Select the Browse button to locate and select the file, then select the Upload button to complete the upload. The file will be checked for consistency and will define the order after successfully passing all tests.
6. Any validation errors encountered in the file will need to be corrected and saved then return to Step 3. For assistance with errors see examples of files can be found below: look in the Comments field of the examples for further tips and information.

Example Of A Correctly Prepared File

PlateID,Row,Column,Organism,Species,Genotype,Tissue,Comments
1,A,1,Barley,Hordeum vulgare L.,genotype 1,leaf,header row (above) must be present in the file
1,B,1,Barley,Hordeum vulgare L.,genotype 2,leaf,genotype name number 2
1,C,1,Barley,Hordeum vulgare L.,genotype 2,leaf,genotype 2 again - names can repeat
2,A,1,Barley,Hordeum vulgare L.,genotype 3,leaf,start of plate 2 (skipping empty wells) - no records for them
2,B,1,Barley,Hordeum vulgare L.,genotype 4,root,tissues (here root) may vary within a file
2,C,1,Barley,Hordeum spontaneum K. Koch,genotype 5,leaf,species names may vary within a file
pl3,A,1,Barley,Hordeum vulgare L.,genotype 6,leaf,start of plate 3 - plate ids do not have to be consecutive numbers
pl3,B,1,Barley,,genotype 7,root,names of Species are not compulsory to provide
pl3,C,3,Barley,Hordeum vulgare L.,genotype 8,leaf,no gaps in wells, samples organized column-wise

Example of Common File Errors

The following records are examples illustrating some of the common data errors.

In each record the comments column describes the error.

The following header row applies for each record.

PlateID,Row,Column,Organism,Species,Genotype,Tissue,Comments

Data Errors

  • Incorrect Tissue Name
2,A,1,Barley,Hordeum vulgare L.,genotype 3,leaves,watch for standard tissue names - should be leaf

Formatting Errors

The following examples illustrate some common formatting errors:

  • Too Many Commas
1,B,1,Barley,Hordeum vulgare L.,genotype,2,leaf,too many commas in line
  • Duplicated Well – Must be Unique
 1,C,1,Barley,Hordeum vulgare L.,genotype 2,leaf,this is a good line
 1,C,1,Barley,Hordeum vulgare L.,genotype 2,leaf,this is also good - but the same well cannot be used twice
  • Illegal Character Usage
2,B,1,Barley,Hordeum vulgare L.,genotype 4,root,this comment 'contains' "forbidden" ; characters
  • No Genotype Name – Missing Mandatory Field
pl3,A,1,Barley,Hordeum vulgare L.,,leaf,genotype name cannot be empty
  • Genotype Name Too Long
pl3,B,1,Barley,,Very Long Genotype Name More Than 100 characters,root,genotype name cannot be longer than 100 characters
  • Data Provided For Well H12
pl3,H,12,Barley,Hordeum vulgare L.,genotype 8,leaf,wells G12 and H12 are not allowed in your file
Page last updated: October 16, 2018, 2:56 pm