Importing & editing experiment sample data

Add or modify columns in your sample data to reflect the different variables in your experiment

Written by Andrew Goodspeed


The sample data table in Pluto provides a flexible container for any annotations and other metadata important to your experiment.

The sample ID column contains unique identifiers for your samples, so each sample occupies one row in the table.

Additional columns can be added to include biologically-relevant metadata such as age, sex, timepoint, dose, and other factors that may be present in your experimental design. These columns can be used to group samples in different ways during analysis.

Creating a sample data table from a CSV

Sample ID column

You can create a sample data from scratch by creating a new .csv file in Excel or a similar program, and listing out sample IDs for your experiment in the first column with a column name of "sample_id" (case insensitive). Each row should have a unique sample ID, which will correspond to the assay data when uploaded. The first column of the sample_data.csv must contain the sample ID.

Metadata columns

In subsequent columns following the sample ID, list out biological factors or variables in your experiment. For example:

  • Age

  • Sex

  • Timepoint

  • Drug

  • Dose

  • Genotype

Whenever possible, try to use metadata columns for only one variable each (the Pluto application will let you combine variables later). For example,

Not recommended:

Recommended format:

The latter, recommended format affords greater flexibility for grouping samples during analysis because grouping could be done by Condition, by Sex, or by Condition+Sex.

FASTQ file columns

If your experiment generated FASTQ files for each sample, include the R1 FASTQ filename (and optionally, the R2 filename) in columns called "r1_fastq" and "r2_fastq."

Sample data templates

For more examples of formatting your sample data, view the template here.

Editing an existing sample data table

Note: Editing the sample data table on an experiment will reset any plots that have already been created. If you have already created plots and need to edit the sample data, we recommend creating a copy of the experiment before editing.

To make changes to the sample data for an experiment, first download the .csv file table using the "..." icon in the upper right corner of the sample data tab.

Open the .csv file in Excel or another data editing program and modify the data as needed. For example, we can add a new column to this experiment called severity that contains a "mild," "moderate" or "severe" annotation for each patient.

Next, select Edit Sample Data from the "..." menu. Click Upload new file and drag and drop in the revised sample data .csv file you edited.

Click continue and wait a few seconds for the data to refresh to see your updated sample data table.