Submit Your Data to CryptoDB

EuPathDB welcomes submissions of genomic-scale data concerning eukaryotic pathogens and host-pathogen interactions. Please review our Data Submission Policy.

Our most common data types include transcriptomics, proteomics, metabolomics, epigenomics, population-level and isolate information. We also accept other genomic-scale data and are open to suggestions. Use the Contact Us link to make suggestions. We look forward to working with you!

 

Data Submission Process:

 

1.     Contact EuPathDB Outreach for an initial review of your data.

Use the Contact Us link to send a brief description (two or three sentences) of your data. We will make every effort to reply quickly. During the data submission process, data sets are scheduled for an upcoming release and given a release date so that we can allocate our resources appropriately. This release date is flexible. Data will not be made available to anyone, used for any other purpose or be made public until you, the data provider, are satisfied that releasing the data is appropriate and the data representation is accurate.

 

 

2.     Submit your Data.   

Find your data type below and expand the section to see specific instructions.

 

High Throughput or Next Generation Sequencing – RNA, DNA or ChIP Sequencing

We prefer to download the raw read data in FASTQ format from a sequence read archive. We integrate your data into the database using the raw reads and use the raw reads during future database releases to remap or update our analyses when necessary.

1.       Transfer a copy of your data to EuPathDB using one of these three options:

o   PREFERRED: Upload your data to a sequence read archive such as DNA Data Bank of Japan, the European Nucleotide Archive or NCBI's Sequence Read Archive. If your data is already submitted to a data repository, there is no need to re-transfer the data to EuPathDB.  In either case, we will retrieve the data directly from the repository. 

o   Upload your data to our ftp site. Use the Contact Us form to request access to our ftp site.

o   Post your data to your ftp site and use the Contact Us form to send us instructions for retrieving your data.

2.       Complete the appropriate data description form making sure to enter your data archive accession numbers (if any) when prompted.

o   RNA Sequencing Data Description Form

o   DNA-Seq Data Description Form

o   ChIP-Sequencing Data Description Form

Microarray

Files (CEL, CSV) should include expression levels and probe set information.

1.       Transfer a copy of your data to EuPathDB using one of these four options:

o   Upload your data to a repository such as Gene Expression Omnibus.

o   Upload your data to our ftp site. Use the Contact Us form to request access to our ftp site.

o   Post your data to your ftp site and use the Contact Us form to send us instructions for retrieving your data.

o   Send your data as an attachment to an email. Use the Contact Us form to send us an email.

 

2.       Complete our Microarray Data Description Form making sure to enter your data archive accession numbers (if any) when prompted. Pay special attention to clearly indicate the identity of columns in the data files you transferred to EuPathDB.

Proteomics

Excel or tab delimited text files are preferred. We can accommodate xml file format. Required columns include gene IDs, peptide sequences, peptide counts and scores.

1.       Transfer a copy of your data to EuPathDB using one of these three options:

o   Upload your data to our ftp site. Use the Contact Us form to request access to our ftp site.

o   Post your data to your ftp site and use the Contact Us form to send us instructions for retrieving your data.

o   Send your data as an attachment to an email. Use the Contact Us form to send us an email.

2.       Complete the Proteomics Data Description Form making sure to clearly indicate the content of each column in your file.

Quantitative Proteomics

Excel or tab delimited files are preferred. We can accommodate xml file format. Required columns include gene IDs and scores.

1.       Transfer a copy of your data to EuPathDB using one of these three options:

o   Upload your data to our ftp site. Use the Contact Us form to request access to our ftp site.

o   Post your data to your ftp site and use the Contact Us form to send us instructions for retrieving your data.

o   Send your data as an attachment to an email. . Use the Contact Us form to send us an email.

2.       Complete the Quantitative Proteomics Data Description Form making sure to include a description of data columns, for example, time course units and arrangement if not apparent from column headers.

 

ChIP-chip

Your data files should include expression levels and probe set information.

1.       Transfer a copy of your data to EuPathDB using one of these four options:

o   Upload your data to a repository such as Gene Expression Omnibus.

o   Upload your data to our ftp site. Use the Contact Us form to request access to our ftp site.

o   Post your data to your ftp site. Use the Contact Us form to send us instructions for retrieving your data.

o   Send your data as an attachment to an email. Use the Contact Us form to send us an email.

o    

2.       Complete the ChIP-chip Data Description Form making sure to enter the archive accession numbers (if any) for your data when prompted. We will retrieve your data from the sequence read archive.

Isolates typed by sequencing limited genetic loci

       If your data IS uploaded to Genbank, use the Contact Us to tell us about your data. Genebank Isolate records and the associated metadata are automatically updated with each EuPathDB release.  There is no need to complete our Isolate Submission Form.

       If your data IS NOT uploaded to Genbank, we can facilitate this upload. Complete the Isolate Submission Form and we will use the information to generate a Genbank submission for your isolates. The new isolate records will be downloaded to EuPathDB with the release. Use the Contact Us form to send us instructions for retrieving your data.

          Isolate Submission Form
          Help for submitting Isolate Data

Isolates or Strains typed by High Throughput Sequencing

We prefer to receive the raw read data in FASTQ or FASTA file format. We integrate your data into the database using the raw reads. We also use the raw reads during future database releases to remap your data when the reference genome is reloaded and to update our analyses when needed.

1.       Transfer a copy of your data to EuPathDB using one of these three options:

o   Upload your data to a sequence read archive such as DNA Data Bank of Japan, the European Nucleotide Archive or NCBI's Sequence Read Archive. We will retrieve your data using the read archive's accession numbers for your data set.

o   Upload your data to our ftp site. Use the Contact Us form to request access to our ftp site.

o   Post your data to your ftp site where we can retrieve the data. Use the Contact Us form to send us instructions for retrieving your data.

2.       Complete our DNA Seq Data Description Form making sure to enter the read archive accession numbers (if any) for your data when prompted. We also ask that you complete an abbreviated Abbreviated Isolate Submission Form to describe meta data associated with your isolates.

Genome Sequence and/or Annotation

We prefer to download annotated genome sequence from a repository which assigns gene IDs, for example, the DNA Data Bank of Japan, the European Nucleotide Archive or NCBI's GenBank.

       If your genome IS uploaded to a repository, complete the Genome Sequence and/or Annotation Description Form making sure to include the accession numbers of your data when prompted. We will download your data from the repository.

       If your data IS NOT uploaded to a repository, use the Contact Us form to tell us about your data and work out the best way to transfer the data.

       If you are submitting only genome annotation (gff, ensemble, gtf or genbank formats), transfer a copy of your files to EuPathDB using one of these three options:

o   Upload your data to our ftp site. Use the Contact Us form to request access to our ftp site.

o   Post your data to your ftp site where we can retrieve the data. Use the Contact Us form to send us instructions for retrieving your data.

o   Send your data as an attachment to an email. Use the Contact Us form to send us an email.

General Data Submission –use for data that does not fit any of the above categories

          Use the Contact Us form to tell us about your data and work out the best way to transfer the data.