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).
- Experiment description (not publication abstract)
- Protocols of all experimental and data analysis procedures
- Sample annotation (as much details as possible)
- Author information
- 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 validation in Annotare was successful you are automatically sent an accession number. The experiment is then curated which may involve further inquiry by email. You may cite this 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.