152 lines
9.3 KiB
HTML
152 lines
9.3 KiB
HTML
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<head>
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<title>Affymetrix submissions - GEO - NCBI</title>
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<li><a href="#">GEO Publications</a>
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<span>Affymetrix submissions</span><span id="login_status"><a href="/geo/submitter/" title="Click here to login. You need to do this only if you want to edit the contact information, submit data, see your unreleased data, or work with data already submitted by you. You do not need to login if you are here just to browse through public holdings">Login</a></span></div>
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<div id="content">
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<h1 title="Affymetrix submissions">Recommendations for Affymetrix submissions</h1>
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<p>
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This page contains deposit recommendations, instructions and templates specific to Affymetrix arrays.
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These recommendations simply describe what we believe is the easiest batch deposit method for the
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majority of Affymetrix researchers, but keep in mind that Affymetrix data may be submitted to GEO
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using any of the deposit options described on the <a href="/geo/info/submission.html">Submitting data</a> page.
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If you need additional guidance for your submission, please <a href="mailto:geo@ncbi.nlm.nih.gov">e-mail us</a>
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with a brief description of the type of data you are trying to submit, and one of
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our curators will quickly get back to you.
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</p>
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<p>
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The <a href="/geo/info/spreadsheet.html">GEOarchive</a> spreadsheet-based submission method is recommended for Affymetrix deposits. <br />
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With this submission option, you provide the following components:
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</p>
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<ol>
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<li>
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<span>
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An Excel metadata worksheet containing descriptive information and
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protocols for the overall experiment and individual Samples (see templates below).
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</span>
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</li>
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<li>
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<span>
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CEL files
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</span>
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</li>
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<li>
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<span>
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Processed data, usually probe set summary data generated by the primary analysis
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software (e.g., Expression Console, Microarray Suite 5.0, Genotyping Console,
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GTYPE/CNAT, GTGS, Tiling Array Software, or GeneChip-compatible/other 3rd-party
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software). These data may be submitted either as CHP files or a
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matrix table (see examples in templates below). Please submit the data used to draw the conclusions of your study.
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For instance, do not submit CHP files analyzed with MAS5.0 if your submission is related
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to a publication based on GC-RMA data. In this case, you should submit the
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GC-RMA probe set summary data instead of MAS5.0 CHP files.
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</span>
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</li>
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</ol>
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<h2>Custom arrays and alternative probe groupings</h2>
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<p>
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You must provide library files (CDF or CLF/PGF) and gene-level probe set annotations when submitting data for custom arrays, or when
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alternative (custom) probe groupings are used. The probe sequences are also required for custom arrays (probe_fasta or probe_tab files).
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The gene-level annotations can be included as additional columns in the matrix table containing the scaled or normalized data, or they can be
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supplied as an external file (e.g. Affymetrix annotation CSV file).
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</p>
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<h2>Affymetrix GEOarchive templates and examples</h2>
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<p>
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The following Excel files illustrate the structure of different types of GEOarchive Affymetrix data submissions.
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Each Excel file consists of several worksheets, including a metadata template, and metadata and matrix table examples.
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Click the tabs at the bottom of the spreadsheet window to switch between worksheets.
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Guidelines for the content of each field is provided on the worksheets.
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</p>
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<ul class="link-list">
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<li><a href="/geo/info/examples/GA_affy_CHP.xls">3' or Whole Gene Expression Array - CHP file option</a></li>
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<li><a href="/geo/info/examples/GA_affy.xls">3' or Whole Gene Expression Array - Matrix table option</a></li>
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<li><a href="/geo/info/examples/GA_affy_Exon_CHP.xls">Exon Array - CHP file option</a></li>
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<li><a href="/geo/info/examples/GA_affy_Exon_Matrix.xls">Exon Array - Matrix table option</a></li>
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<li><a href="/geo/info/examples/GA_affy_genomic_BAR.xls">Tiling Array</a></li>
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<li><a href="/geo/info/examples/GA_affy_SNP.xls">SNP Array</a></li>
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</ul>
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<div class="deposit">
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<p>
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Bundle all components (Excel metadata file, CEL files, CHP files or matrix table,
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plus library/sequence/annotation files for custom applications) together into a .zip, .rar, or
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.tar archive using a program like WinZip, and transfer to GEO using the <a href="https://submit.ncbi.nlm.nih.gov/geo/submission/">Submit to GEO</a> page.
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Incomplete submissions will result in processing delays.
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</p>
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<div class="submit_button">
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<a href="https://submit.ncbi.nlm.nih.gov/geo/submission/">Submit</a>
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</div>
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</div>
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</div>
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</div>
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<div id="last_mod">
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Last modified: July 16, 2024</div>
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<div id="footer">
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<span class="helpbar">|<a href="https://www.nlm.nih.gov"> NLM </a>|<a href="https://www.nih.gov"> NIH </a>|<a href="mailto:geo@ncbi.nlm.nih.gov"> Email GEO </a>|<a href="/geo/info/disclaimer.html"> Disclaimer </a>|<a href="https://www.nlm.nih.gov/accessibility.html"> Accessibility </a>|<a href="https://www.hhs.gov/vulnerability-disclosure-policy/index.html"> HHS Vulnerability Disclosure </a>|
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