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RNA-seq and ChIP-seq data
1. Types of data that can be submittedArrayExpress accepts submissions of non-human and human non-identifiable RNA-seq and ChIP-seq data. To submit to ArrayExpress, all you need to do is fill in a simple spreadsheet and transfer your data files to us. We will transfer the raw data files to the European Nucleotide Archive for you. If you have human potentially-identifiable sequencing data you need to submit to the European Genome-phenome Archive (EGA) and not ArrayExpress. They will supply you with a template for submission and store human identifiable data securely. They will then pass the non-identifiable data to us as shown in the diagram below.
Diagram of the submission of different sequencing data types to ArrayExpress or the European Genome-phenome archive.
2. How to submit your dataTo submit data to us, fill out a simple spreadsheet with sample and protocol information and transfer your trace data files for each sample and any processed data files to us through our spreadsheet submission system web page. The spreadsheet format we use is called MAGE-TAB. To create a spreadsheet template based on some general information about your experiment and then submit it to ArrayExpress:
Alternatively fill out the basic spreadsheet template for a sequencing experiment here: sequencing template and upload this through the spreadsheet submission system as described above. We can also help you to create a template spreadsheet and answer any questions you may have about filling it out. Please email us at miamexpress@ebi.ac.uk. If you have both sequencing and microarray-based data please create a spreadsheet for each and submit them as separate 'experiments' even if they are related. Our processing of the two types of data is slightly different. If you have a large amount of data to submit please transfer your files by FTP to us instead of uploading it through the spreadsheet submission system web page. Please email us to tell us you are doing this so that we can identify your files on the FTP site.
3. Which data files to submitSubmit the trace data files and any processed data files that you have e.g. files in which the expression values are linked to genome coordinates. The trace data files that you submit to ArrayExpress will be stored in the European Nucleotide Archive (ENA). The following trace data file formats are accepted:
Fastq format files are also accepted, but SRF format files are preferred. These are developing technologies and these recommendations may change. Please contact us with any questions for help or further information on submission of RNA-seq and ChIP-seq data.
4. Example RNA-seq/ChIP-seq submission spreadsheets and experiments in ArrayExpressRNA-seq exampleIllumina Solexa RNA-Seq experiment - E-MTAB-197 ChIP-Seq exampleIllumina Solexa ChIP-Seq experiment - E-MTAB-115
If you have any questions about submitting RNA-seq or ChIP-seq data or would like help creating a spreadsheet please contact us at miamexpress@ebi.ac.uk. |
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