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<b><span style="font-size:16.0pt">How to get NGS data from EBML-EBI in to the Xenbase-GEO pipeline.<o:p></o:p></span></b></p>
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<b><span style="font-size:16.0pt"><br>
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<p style="background-image: initial; background-"><span style="font-family: Cambria, serif;">Xenbase NGS pipeline processes RNA-Seq and ChIP-seq data from the NCBI's GEO archive so that it is searchable, comparable and can be viewed on JBrowse: see
</span><a href="http://www.xenbase.org/geneExpression/gseCurationSearch.do?method=search" target="_blank" id="LPlnk616657" class="OWAAutoLink" previewremoved="true"><span style="font-family:"Cambria",serif;mso-fareast-font-family:
"Times New Roman";mso-bidi-font-family:Calibri;color:blue">http://www.xenbase.org/geneExpression/gseCurationSearch.do?method=search</span></a><span style="font-family: Cambria, serif;">).</span><o:p></o:p></p>
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<span style="font-family: Cambria, serif; background-image: initial; background-">It is important to know that NGS data that has been<b> deposited with the EBI, is shared with the NCBI's BIOProject
</b>database, but that it </span><b><i><span style="font-family: Cambria, serif; background-image: initial; background-">does not</span></i></b><span style="font-family: Cambria, serif; background-image: initial; background-"> then migrate automatically to
GEO, and therefore Xenbase will <b>NOT</b> be able to automatically process your RNA-seq data. <o:p></o:p></span></p>
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<span style="font-family: Cambria, serif; background-image: initial; background-"><o:p> </o:p></span></p>
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<span style="font-family: Cambria, serif; background-image: initial; background-">So how can you get your NGS data into GEO if you have already submitted it to EMBL-EBI?</span><span style="font-family:"Times New Roman",serif;
mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
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<o:p> </o:p></p>
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<!--[if !supportLists]--><span style="font-size:11.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
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</span></span><!--[endif]--><b><span style="font-size:11.0pt;font-family:"Tahoma",sans-serif;mso-fareast-font-family:
"Times New Roman";color:#212121">Authors need to submit both metadata and processed data directly to GEO</span></b><span style="font-size:11.0pt;
font-family:"Tahoma",sans-serif;mso-fareast-font-family:"Times New Roman";
color:#212121">.<o:p></o:p></span></p>
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<span style="font-size:11.0pt;font-family:"Tahoma",sans-serif;mso-fareast-font-family:
"Times New Roman";color:#212121"><o:p> </o:p></span></p>
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<!--[if !supportLists]--><span style="font-size:11.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
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</span></span><!--[endif]--><span style="font-size:11.0pt;font-family:"Tahoma",sans-serif;mso-fareast-font-family:
"Times New Roman";color:#212121"><b>Instructions for submitting sequencing data to GEO are here</b>:
</span><a href="https://www.ncbi.nlm.nih.gov/geo/info/seq.html" target="_blank" id="LPlnk658859" class="OWAAutoLink" previewremoved="true"><span style="font-size:11.0pt;font-family:"Tahoma",sans-serif;
mso-fareast-font-family:"Times New Roman";color:blue">https://www.ncbi.nlm.nih.gov/geo/info/seq.html</span></a><span style="font-size:11.0pt;font-family:"Tahoma",sans-serif;mso-fareast-font-family:
"Times New Roman";color:#212121"><o:p></o:p></span></p>
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<span style="font-size:11.0pt;
font-family:"Tahoma",sans-serif;mso-fareast-font-family:"Times New Roman";
color:#212121"><o:p> </o:p></span></p>
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<!--[if !supportLists]--><b><span style="font-size:11.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
mso-bidi-font-family:Symbol;color:#212121">·<span style="font-variant-numeric: normal; font-variant-east-asian: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: "Times New Roman";">
</span></span><!--[endif]--></b><span style="font-size:11.0pt;font-family:"Tahoma",sans-serif;mso-fareast-font-family:
"Times New Roman";color:#212121"><b>Access the Metadata template here<br>
</b>(</span><a href="https://www.ncbi.nlm.nih.gov/geo/info/examples/seq_template_v2.1.xls" target="_blank" id="LPlnk675301" class="OWAAutoLink" previewremoved="true"><span style="font-size:11.0pt;font-family:"Tahoma",sans-serif;
mso-fareast-font-family:"Times New Roman";color:blue">https://www.ncbi.nlm.nih.gov/geo/info/examples/seq_template_v2.1.xls</span></a><span style="font-size:11.0pt;font-family:"Tahoma",sans-serif;mso-fareast-font-family:
"Times New Roman";color:#212121">)
<o:p></o:p></span></p>
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<span style="font-size:11.0pt;font-family:"Tahoma",sans-serif;mso-fareast-font-family:
"Times New Roman";color:#212121"><o:p> </o:p></span></p>
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<!--[if !supportLists]--><span style="font-size:11.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
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</span></span><!--[endif]--><span style="font-size:11.0pt;font-family:"Tahoma",sans-serif;mso-fareast-font-family:
"Times New Roman";color:#212121"><b>You
</b><i style="font-weight: bold;">do not</i><b> need to re-submit the raw data files. </b><b> </b></span><span style="color: rgb(33, 33, 33); font-family: Tahoma, sans-serif; font-size: 11pt; text-indent: 0.25in;"><b>Instead, include the following additional
information in the Metadata template</b>.</span></p>
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<span style="font-size:11.0pt;font-family:"Tahoma",sans-serif;
mso-fareast-font-family:"Times New Roman";color:#212121"><o:p> </o:p></span></p>
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<span style="font-size:11.0pt;
font-family:"Tahoma",sans-serif;mso-fareast-font-family:"Times New Roman";
color:#212121"><br>
[1] Reference the SRA Study accession (SRPnnnn) and BioProject accession<br>
(PRJNAnnnn) in the SERIES 'Overall design' field.<br>
<br>
[2] In the 'raw file' column of the SAMPLES section, please list the corresponding SRA Experiment accessions (SRXnnnnnn) so that we can create the appropriate links between the SRA Experiments and GEO Samples.
<o:p></o:p></span></p>
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<span style="font-size:11.0pt;
font-family:"Tahoma",sans-serif;mso-fareast-font-family:"Times New Roman";
color:#212121"> <br>
[3] Add a 'BioSample' column to the SAMPLES section and include the corresponding BioSample accessions (SAMNnnnnnn).<br>
<br>
[4] Add an 'instrument model' column to the SAMPLES section and indicate the<br>
instrument model that was used for sequencing.<br>
<br>
You do not need to fill in the 'RAW FILES' or 'PAIRED-END EXPERIMENTS' <br>
sections.<br>
<br>
[5] Please upload the Metadata template and processed data files to GEO.<br>
FTP instructions for depositing sequencing data to GEO are here:<br>
</span><a href="https://www.ncbi.nlm.nih.gov/geo/info/seq.html#data" target="_blank" id="LPlnk886309" class="OWAAutoLink" previewremoved="true"><span style="font-size:11.0pt;font-family:"Tahoma",sans-serif;
mso-fareast-font-family:"Times New Roman";color:blue">https://www.ncbi.nlm.nih.gov/geo/info/seq.html#data</span></a><span style="font-size:11.0pt;font-family:"Tahoma",sans-serif;mso-fareast-font-family:
"Times New Roman";color:#212121"><br>
<br>
[6] If you have previously contacted GEO and received an email reply from them [ie from geo@ncbi.nlm.nih.gov,] please reference the issue/ticket number the NCBI tracking system gave you [eg #29999555) so that the curator processing your submission is aware
of any correspondence.</span></p>
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<p style="margin-top:0;margin-bottom:0">Several researchers have already followed these steps and reportedit was easy and straighforward, but p<span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">lease
let Xenbase know if you have any trouble: Xenbase@ucalgary.ca</span></p>
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