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Data submission to AE

Data submission to AE. Data submission to AE www.ebi.ac.uk/microarray/submissions.html. MAGE-TAB Example. MAGE-TAB Submission. Ontology Link. Submitter is directed to either submit an experiment or download a template to the desktop. MAGE-TAB Submission.

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Data submission to AE

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  1. Data submission to AE ArrayExpress

  2. Data submission to AEwww.ebi.ac.uk/microarray/submissions.html ArrayExpress

  3. MAGE-TAB Example ArrayExpress & Atlas

  4. MAGE-TAB Submission Ontology Link Submitter is directed to either submit an experiment or download a template to the desktop ArrayExpress & Atlas

  5. MAGE-TAB Submission ArrayExpress & Atlas

  6. Submission of HTS gene expression data • Submit via MAGE-TAB submission route • Submit: • MAGE-TAB spreadsheet containing details of the samples and protocols used. • Trace data files for each sample (in SRF, FASTQ or SFF format ) • Processed data files  • For non-human species we will supply your SRF or FASTQ files to the European Nucleotide Archive (ENA). • If you have human identifiable sequencing data you need to submit to the The European Genome-phenome Archive and not ArrayExpress. They will supply you with a suitable template for submission and store human identifiable data securely. ArrayExpress & Atlas

  7. Types of data that can be submitted ArrayExpress & Atlas

  8. MAGE-TAB Example: IDF Value indicating which sequencing instrument was used (e.g. 454 GS, Illumina Genome Analyzer, AB SOLiD System).

  9. MAGE-TAB Example: SDRF

  10. MAGE-TAB Example: SDRF ArrayExpress & Atlas

  11. What needs to be included in the Spreadsheet? • Include Assay Name and Technology Type columns • Raw files must go in the Array Data File column • A sequencing protocol must be provided. • The sequencing protocol should have a performer- this is used as the run center name. • This protocol must have a Protocol Hardware value saying which sequencing instrument was used (e.g. 454 GS, Illumina Genome Analyzer, AB SOLiD System • Reference this in the Protocol REF column before the Assay Name column. • These 4 extra Comment[] columns should be added after Extract Name to provide information about how the library was prepared • Comment[LIBRARY_LAYOUT]- either SINGLE or PAIRED • Comment[LIBRARY_SOURCE]- one of GENOMIC, NON GENOMIC, SYNTHETIC, VIRAL RNA, OTHER • Comment[LIBRARY_STRATEGY] - one of WGS, WCS, CLONE, POOLCLONE, AMPLICON, BARCODE, CLONEEND, FINISHING, ChIP-Seq, MNase-Seq, EST, FL-cDNA, CTS, OTHER • Comment[LIBRARY_SELECTION]- one of RANDOM, PCR, RANDOM PCR, RT-PCR, HMPR, MF, CF-S, CF-M, CF-H, CF-T, MSLL, cDNA, ChIP, MNase, other, unspecified ArrayExpress & Atlas

  12. Platform Specific Attributes Include the following attributes as Comment[] columns after Assay Name: • For LS454: • KEY_SEQUENCE (string - The first bases that are expected to be produced by the challenge bases) • FLOW_SEQUENCE (value is a string, e.g. TACG) • FLOW_COUNT (value is an integer) • For Illumina: • SEQUENCE_LENGTH (integer - The fixed number of bases expected in each raw sequence, including both mate pairs and any technical reads.) • For Helicos: • FLOW_SEQUENCE • FLOW_COUNT • For ABI SOLID: • SEQUENCE_LENGTH (integer - The fixed number of bases expected in each raw sequence, including both mate pairs and any technical reads.) ArrayExpress & Atlas

  13. MAGE-TAB Submission Indicate submission type Ontology Link Submitter is directed to either submit an experiment or download a template to the desktop ArrayExpress & Atlas

  14. MAGE-TAB Submission ArrayExpress & Atlas

  15. What happens after submission? MAGE-TAB spreadsheet, raw and processed data files MTAB to SRA conversion script Submit Curation MAGE-TAB, processed data SRA XML, raw data ENA ArrayExpress Archive Linked by accessions

  16. What happens after submission? • Email confirmation • Curation • The curation team will review your submission and will email you with any questions. • Possible reopening for editing • We will send you an accession number when all the required information has been provided. • We will load your experiment into ArrayExpress and provide you with a reviewer login for viewing the data before it is made public. ArrayExpress & Atlas

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