Formatting sample annotations for experiments with multiple antibodies

Create one experiment in Pluto for each antibody in your ChIP-seq or CUT&RUN experiment

Written by Rani Powers, PhD


For epigenetics experiments like ChIP-seq or CUT&RUN, you may have multiple target antibodies, in addition to a control antibody (often IgG). In Pluto, you'll create one experiment for each target antibody, which will contain the FASTQ files and sample annotations relevant to those samples.


Step 1: Create project

Create a new project in Pluto to contain all of the experiments, one per antibody. Give this project an informative name based on your cell line, model system, treatment, or the hypothesis you are studying.



Step 2: Create one experiment per target antibody

For each target antibody in your experiment, create a new experiment in the project that you created. We recommend including the antibody in the experiment name, as shown in the example above.


On the assay data upload step, upload the FASTQ files for samples in which the target antibody or matching control (IgG) were used.


In the sample data upload step, upload a table containing only the samples for one target antibody, along with the applicable, matched controls.


Step 3: Configure pipeline

In the last step, configure a pipeline run with your desired parameters and click Run pipeline. This will align the FASTQ files you uploaded to the selected genome, perform QC, and generate a consensus peak counts table for the target antibody present in your experiment.




In this study, 3 antibodies were used: H3K4me3, anti-MLL C, and anti-Biotin. There were 10 samples in total:


Because there are 3 different target antibodies, 3 experiments need to be created in Pluto splitting these samples into 3 different sample data tables:


Note that the IgG controls were reused in all 3 experiments



Anti-MLL C