153 lines
8.8 KiB
HTML
153 lines
8.8 KiB
HTML
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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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>Illumina submissions - GEO - NCBI</title>
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<meta name="keywords" content="NCBI, national institutes of health, nih, database, archive, central, bioinformatics, biomedicine, geo, gene, expression, omnibus, chips, microarrays, oligonucleotide, array, sage, CGH" />
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<meta name="description" content="Gene Expression Omnibus (GEO) is a database repository of high throughput gene expression data and hybridization arrays, chips, microarrays." />
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<div id="all">
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<div id="page">
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</a>
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<a href="/geo/"><img src="/geo/img/geo_main.gif" alt="GEO Logo" /></a>
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<div id="nav_bar">
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<ul id="geo_nav_bar">
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<li><a href="#">GEO Publications</a>
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<ul class="sublist">
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<li><a href="/geo/info/GEOHandoutFinal.pdf">Handout</a></li>
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<li><a href="/pmc/articles/PMC10767856/">NAR 2024 (latest)</a></li>
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<li><a href="/pmc/articles/PMC99122/">NAR 2002 (original)</a></li>
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<li><a href="/pmc/?term=10767856,4944384,3531084,3341798,3013736,2686538,2270403,1669752,1619900,1619899,539976,99122">All publications</a></li>
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</ul>
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<li><a href="/geo/info/faq.html">FAQ</a></li>
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<li><a href="/geo/info/MIAME.html" title="Minimum Information About a Microarray Experiment">MIAME</a></li>
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<li><a href="mailto:geo@ncbi.nlm.nih.gov">Email GEO</a></li>
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</ul>
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<div id="crumbs_login_bar"><a title="NCBI home page" href="/">NCBI</a> »
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<a id="curr_page" title="GEO home page" href="/geo/">GEO</a> »
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<a title="GEO documentation guide" href="/geo/info/">Info</a> »
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<span>Illumina 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="Illumina submissions">Recommendations for Illumina submissions</h1>
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<p>
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This page contains deposit recommendations, instructions and templates
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specific to Illumina <i>arrays</i> (for Illumina <i>sequence</i> deposits, please go to
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<a href="/geo/info/seq.html">Submitting High-throughput Sequence Data</a> instructions).
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These recommendations simply describe what we believe is the easiest batch deposit method
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for the majority of Illumina researchers, but keep in mind that Illumina array data may
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be submitted to GEO using any of the deposit options
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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
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<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>
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spreadsheet-based submission method is recommended for Illumina array deposits.
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</p>
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<p>
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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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A Metadata worksheet containing descriptive information and protocols for the overall experiment and individual Samples.
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</li>
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<li>
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A Matrix worksheet containing the final processed/normalized data used
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to draw the conclusions from your study (e.g., cubic spline).
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If the processed data row count exceeds Excel's limit, please supply
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your Matrix as a tab-delimited, plain-text file (.txt).
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</li>
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<li>
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IDAT files containing the raw data.
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You are also welcome to submit a text file containing non-normalized data.
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</li>
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</ol>
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<h2>Finding the Platform</h2>
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<p>
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On the metadata worksheet you are asked to specify what array (Platform) you used.
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Most commercial Illumina arrays are already represented in GEO,
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to find the accession number (GPLxxx) use the
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<a href="/geo/browse/?view=platforms&tool=findplatform&manufacturer=Illumina">FIND PLATFORM</a> tool.
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Please use Illumina's <b>GEO Data Submission Report Plug-in for Gene Expression</b>
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(<a href="https://support.illumina.com/array/array_software/genomestudio/downloads.html">download</a>)
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to format the normalized and raw data generated by BeadStudio.
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For issues related to the plug-in, please contact Illumina's technical support department at
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<a href="mailto:techsupport@illumina.com">techsupport@illumina.com</a>.
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</p>
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<h2>Illumina 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 Illumina data submissions.
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Each Excel file consists of several worksheets, including a metadata template, and metadata and matrix 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_illumina_expression.xls">gene expression data</a></li>
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<li><a href="/geo/info/examples/GA_illumina_genotype.xls">genotype data</a></li>
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<li><a href="/geo/info/examples/GA_illumina_methylation.xlsx">methylation data</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, unnormalized and processed matrix tables) together
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into a .zip, .rar, or .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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