Experiment submissions overview
Annotare webform tool
Read this guide before submitting
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- For all non-pipeline submissions of microarray or sequencing experiments. Pipeline submitters: please contact us at firstname.lastname@example.org and we will advise further
- Fill in a series of webforms (auto-saved), featuring auto fill-down and copy/paste ("import values") functions
- Supports up to 1000 assays, no complex design (e.g. one microarray design used, no sample pooling)
- Upload data files directly within the tool or via FTP
- Automatic validation prior to submission to speed up downstream processing and loading into ArrayExpress
- Supports double-blind peer review in downstream processing, by hiding submitter's contact information from reviewers
ArrayExpress accepts all functional genomics data, e.g. expression profiling, genotyping, chromatin immunoprecipitation, copy-number variation, from microarray and sequencing technologies.
Microarray submissions follow the "Minimum Information About a Microarray Experiment" (MIAME) guidelines, while sequencing submissions follow a similar set of guidelines, "Minimum Information About a Sequencing Experiment" (MINSEQE).
Data from human samples and individuals that can potentially lead to the identification of the donors (e.g. genomic DNA sequences) can be submitted to ArrayExpress if the data has been consented for public release. Such approvals typically would be given by the relevant ethics committees and ensuring this is the responsibility of the submitters. Identifiable data approved for controlled access should be submitted to the European Genome-phenome Archive (EGA) (more details here).
Following the MIAME/MINSEQE guidelines, we ask submitters to provide:
Meta-data: E.g. Background biology of your experiment, aim of the experiment, biological materials/samples used and their characteristics, wet-lab and dry-lab procedures (protocols).
Raw data files: These are unprocessed data files obtained from the microarray scanner (e.g. Affymetrix CEL files, Agilent feature extraction files) or from the sequencing machine (e.g. fastq files).
- Microarray experiment: Make sure the format of your raw data files matches one of the accepted formats.
- Sequencing experiment: Make sure your raw sequence read files are prepared according to specifications by the European Nucleotide Archive (ENA) and send them to ArrayExpress by FTP. You'll also need to gather details about your samples/libraries/data files. For more details, see this specific help page on sequencing submissions.
Processed data files: These are data files generated from the raw data files, often involving e.g. normalisation or background-subtraction. In sequencing experiments, the processing can also involve alignment of sequencing reads to a reference genome, calculation of RPKM/FPKM values, etc.
- Microarray experiment: Send us processed data in tab-delimited text (*.txt) files (not Excel spreadsheets) as in this this guide.
- Sequencing experiment: We accept tables/spreadsheets of processed data saved as tab-delimited text (*.txt) format. We also accept bam (alignment) files, see bam file specification for more details.