submission process in the ArrayExpress repository

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1. Prepare Your Data
   Before starting the submission, you will need to ensure that your data and metadata are organized and follow the standards expected by ArrayExpress. Here's what you need:

Raw data: FASTQ or other raw sequencing files generated from your Tn-Seq experiment.
Processed data (optional): If you have analyzed or processed data (e.g., a table of transposon insertion sites), you can submit this as well.
Metadata: Detailed information about the experiment, which includes:
Study details: Description of the overall study, including the purpose, biological system (budding yeast in your case), and experimental design.
Sample information: Information on each biological replicate or sample used in the experiment.
Experimental protocols: Descriptions of the sequencing and transposition protocols used, including the library preparation, sequencing platform, and any other relevant experimental details.

2. Register for an Account
   If you don't already have an account with EMBL-EBI, you will need to create one. Follow these steps:

Go to the ArrayExpress login page: ArrayExpress Login.
Register for a new account by clicking on "Sign up for an account."
Complete the registration form, confirm your email, and log in.

3. Start the Submission Process
   Once logged in, you can begin the submission process:

Go to the ArrayExpress Submission Page: Navigate to ArrayExpress submissions.
Click on “Submit your data” and select the type of experiment you're submitting (e.g., RNA-seq, microarray, or sequencing). For Tn-Seq, you'll choose the "RNA-seq" or "other sequencing" options, as they are appropriate for functional genomics sequencing data.

4. Complete the Submission Forms
   You'll be required to fill out a series of forms detailing your experiment. Here’s what you’ll need to provide:

Experiment Description: Provide a summary of your Tn-Seq experiment, explaining the goals, biological system (budding yeast), and conditions tested.
Organism: Select the organism (Saccharomyces cerevisiae) as the organism of interest.
Experimental Factors: Input key experimental variables such as the condition (e.g., gene knockout, environmental stress) and other relevant metadata.
Sample Information: For each sample, provide the sample name, organism, cell type, treatment (if applicable), and any other relevant conditions.
Protocol Information: Input detailed protocols for library preparation, sequencing, and any sample treatments.

5. Upload Data
   ArrayExpress requires both raw and (optionally) processed data to be uploaded. You’ll need to:

Raw Data (FASTQ files): Upload the raw sequencing data from your Tn-Seq experiment (e.g., FASTQ files). If your data is already deposited in ENA, you can link to it rather than re-upload.
Processed Data (optional): If you have processed data, such as tables listing the mapped transposon insertions, upload these as well.
Data can be uploaded through the Aspera transfer protocol, which is recommended for large datasets. ArrayExpress provides detailed instructions for this in their submission guide.

6. Assign Accession Numbers
   Once you complete the submission form and data upload, ArrayExpress will assign you an accession number. This is a unique identifier that you can use to reference your dataset in publications.

7. Submit and Review
   Before final submission, you can review all the details and ensure everything is correct. Once submitted, the ArrayExpress curation team will review your submission to ensure compliance with metadata standards and completeness.

Post-submission: You will receive confirmation, and your data will be processed. You may be contacted if any additional information is required.
Public release: After curation and acceptance, your data will be made publicly available, typically within a few weeks.
Helpful Links:
ArrayExpress Submission Guide: Submission Guide
Aspera File Transfer Tool: Aspera Transfer Instructions