162 lines
9.4 KiB
HTML
162 lines
9.4 KiB
HTML
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<title>Agilent submissions - GEO - NCBI</title>
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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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<li><a href="#">GEO Publications</a>
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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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<a title="GEO documentation guide" href="/geo/info/">Info</a> »
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<span>Agilent 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="Agilent submissions">Recommendations for Agilent submissions</h1>
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<p>
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This page contains deposit recommendations, instructions and templates specific to Agilent 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 Agilent researchers, but keep in mind that Agilent data may be submitted to GEO using
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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
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submission method is recommended for Agilent 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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A Metadata worksheet containing descriptive information and protocols
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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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Raw data files (unedited). Usually, these will be Agilent Feature
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Extraction result text files. GPR files are also acceptable if they include
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the Agilent Probe Names (e.g., A_23_P158231).
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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/normalized data used to draw the conclusions from your study.
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Two-color experiments (e.g., Cy3/Cy5) will typically have log (test/control)
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ratios; one-color experiments will have normalized signal intensities.
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Processed data should be provided as a value matrix containing data for all
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Samples. Data can be provided in an Excel worksheet or a tab-delimited text file.
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The table should include the Agilent Probe Names (e.g., A_23_P158231).
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</span>
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</li>
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</ol>
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<h2>Finding the Platform <a class="arrow" href="#top" title="Back to top">Back to top</a></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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If you are using a commercial array, include the 6-digit Agilent Design ID (Agilent-nnnnnn)
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or the GEO Platform accession number. If you are using a custom array not represented in GEO,
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download the file in "GEO" format from the <a href="https://earray.chem.agilent.com/earray/">Agilent eArray</a>
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or <a href="http://www.agilent.com/genomics/suredesign">SureDesign</a> website (contact Agilent for instructions)
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and include it with your submission.
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</p>
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<p>
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The GEO accession number of an Agilent platform can be retrieved using the
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<a href="/geo/browse/?view=platforms&tool=findplatform&manufacturer=Agilent">FIND PLATFORM</a> tool.
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It is recommended that you use keyword "Agilent-nnnnnn" in the Free text box where nnnnnn represents
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the 6-digit Agilent Design ID (e.g., Agilent-014850).
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</p>
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<h2>Agilent GEOarchive templates and examples <a class="arrow" href="#top" title="Back to top">Back to top</a></h2>
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<p>
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The following Excel files illustrate the structure of different types of GEOarchive Agilent 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 are provided on the worksheets.
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</p>
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<ul class="link-list">
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<li>
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<a href="/geo/info/examples/GA_Agilent_two_color_matrix.xls">Two-color experiment</a>
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</li>
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<li>
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<a href="/geo/info/examples/GA_Agilent_one_color_matrix.xls">One-color experiment</a>
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</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, raw files, and processed files or matrix table) together into
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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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