Before publishing your study, you need to make the raw sequencing runs avaliable in the NCBI Sequence Read Archive. This directory contains the code and instructions to do this. The recommended way to organize your experiments on the SRA is as follows:
BioProject: Variant Library (i.e Omicron BA.1)
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|___BioSamples: PacBio Barcoding, Individual Studies
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|___SRA Experiments: Individual Runs of Antibodies, Sera, etc..
This structure is in keeping with the scheme used for Yeast Display DMS projects like this one here. For example, here is this structure captured in a single run from BioProject to an individual SRA Experiment:
BioProject >> BioSample >> SRA Experiment
To upload your samples to the SRA, follow along with the code and instructions in the instructions.ipynb Jupyter notebook. This notebook will walk you through how to configure this directory, interact with the SRA, and prepare your sequencing runs for submission.