I would like to submit...
1. What data sets can be submitted?
ArrayExpress accepts all functional genomics data generated from microarray or next-generation sequencing (NGS) platforms. Popular experiment types are transcription profiling (mRNA and miRNA), SNP genotyping, chromatin immunoprecipitation (ChIP) and comparative genomic hybridisation. Here is the full list of experiment types in ArrayExpress.
We currently don't accept metagenomics/metatranscriptomics data (please submit to the EBI Metagenomics service) or de novo transcriptome assembly data (the raw RNA-seq reads should be submitted to ArrayExpress, but the assembled transcriptome file directly to the European Nucleotide Archive).
2. What do I need to prepare?
Breadth of the data and metadata
The aim is that an ArrayExpress user should have everything they need for the data set to make sense and be reproducible without referring to an associated paper.
Microarray submissions follow the "Minimum Information About a Microarray Experiment" (MIAME) guidelines. Sequencing submissions follow a similar set of guidelines, "Minimum Information About a Sequencing Experiment" (MINSEQE).
As a submitter, you may need to consult with your colleagues, e.g. collaborators or the core facility personnel performing microarray hybridisation or sequencing for you, to gather all detailed information for a successful submission.
- Experiment description to give context to the data set (not pasting publication abstract please)
- Protocols of all experimental (e.g. sample sourcing, sequencing library preparation) and data analysis procedures
- Sample annotation (as much details as possible, e.g. age of the plant, mouse strain, cell type)
- Author information (please include the principal investigator of the project)
- Sequencing library specification (NGS experiments only)
- Unprocessed data files
Microarray: files obtained from the microarray scanner (e.g. Affymetrix CEL files, Agilent feature extraction txt files, Illumina idat files)
See the full list of accepted microarray raw data files.
Sequencing: compressed raw sequence read files (e.g. fastq.gz files)
See accepted sequencing raw data files.
- Processed data matrix in tab-delimited txt format
- Other processed data formats, e.g. bam alignment files (optional)
3. The submission process
Experiment submissions are handled via the online tool Annotare, which involves filling in a series of web-forms and direct upload of files.
Before starting, have a look at the pre-submission checklist (because there are a few exceptional cases that need further instructions).
Note that once you have pressed "Submit", you cannot make any further changes. Updating an experiment that is already curated and loaded into ArrayExpress can be tedious and lengthy (especially for sequencing experiments), so please get your submission in the best possible shape before you submit.
4. The curation process
When you pass validation in Annotare and submit the experiment, you are automatically sent an accession number, usually within 15 minutes. (It does depend on how busy our submission processing system is on a given day, and the size of your data files.) The experiment is then in curation, a process which can take up to 5-10 working days, depending on the complexity of your submission and whether major improvements are required. The curator will follow up with you by email if necessary. You may cite the accession number in your publication but be aware that it is your responsibility to ensure that the submission process is completed before the manuscript is published.
5. Success / After the submission
When curation is completed the experiment is loaded into ArrayExpress, which is confirmed by an email from one of our curators. The experiment may stay private with restricted access (e.g. the submitter or journal editors/reviewers can view the data) until the associated research article is published.
The last step will be to release the experiment and add the publication details to your submission. This can be done using the Access Control tool. Login details will have been sent to you by email.