<table><tbody><tr><td><table cellpadding="2" cellspacing="0" width="600"><tbody><tr bgcolor="#cccccc" valign="top"><td colspan="2"><table width="600"><tbody><tr><td><strong class="acc" id="GSE275159"><a href="/geo/query/acc.cgi?acc=GSE275159" onmouseout="onLinkOut('HelpMessage' , geo_empty_help)" onmouseover="onLinkOver('HelpMessage' , geoaxema_recenter)">Series GSE275159</a></strong></td>

<td></td>

<td align="right" onmouseout="onLinkOut('HelpMessage' , geo_empty_help)" onmouseover="onLinkOver('HelpMessage' , geoaxema_gds)"><a href="/gds/?term=GSE275159[Accession]">Query DataSets for GSE275159</a></td>

</tr></tbody></table></td></tr>

<tr valign="top"><td>Status</td>

<td>Public on Nov 05, 2024</td>

</tr>

<tr valign="top"><td nowrap="">Title</td>

<td style="text-align: justify">Classification of pediatric soft and bone sarcomas using DNA methylation-based profiling</td>

</tr>

<tr valign="top"><td nowrap="">Organism</td>

<td><a href="/Taxonomy/Browser/wwwtax.cgi?mode=Info&amp;id=9606" onmouseout="onLinkOut('HelpMessage' , geo_empty_help)" onmouseover="onLinkOver('HelpMessage' , geoaxema_organismus)">Homo sapiens</a></td>

</tr>

<tr valign="top"><td nowrap="">Experiment type</td>

<td>Expression profiling by high throughput sequencing<br></td>

</tr>

<tr valign="top"><td nowrap="">Summary</td>

<td style="text-align: justify">Pediatric sarcomas present heterogeneous morphology, genetics and clinical behavior posing a challenge for an accurate diagnosis. DNA methylation is an epigenetic modification that coordinates chromatin structure and regulates gene expression, determining cell type and function. DNA methylation-based tumor profiling classifier for sarcomas (known as sarcoma classifier) from the German Cancer Research Center (Deutsches Krebsforschungszentrum) was applied to 122 pediatric sarcomas referred to a reference pediatric oncology hospital. The classifiers reported 88.5% of agreement between histopathological and molecular classification confirming the initial diagnosis of all osteosarcomas and Ewing sarcomas. Transcriptome raw data quality was verified with FASTQC. We used STAR-fusion to identify and annotate fusion transcripts based on discordant read alignments with default configurations. ChimeraViz was used to plot fusion-genes.<br></td>

</tr>

<tr valign="top"><td nowrap="">&nbsp;</td>

<td></td>

</tr>

<tr valign="top"><td nowrap="">Overall design</td>

<td style="text-align: justify">RNA was extracted with RNeasy Kit (QIAGEN, Hilden, Germany; cat. ID: 74106) and quantified with High Sensitivity Qubit™ RNA Assay Kits (Invitrogen™, Waltham, MA, USA; cat. ID: Q32855). Transcriptome assay was performed using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina, San Diego, CA, USA) and sequenced on the NextSeq550 or NOVAseqX (Illumina Inc, San Diego, CA, USA). Paired-end runs were sequenced in 74 cycles per read (2 X 74), with an average of 41.5 million reads per sample.<br></td>

</tr>

<tr valign="top"><td nowrap="">&nbsp;</td>

<td></td>

</tr>

<tr valign="top"><td>Contributor(s)</td>

<td><a href="/pubmed/?term=Maschietto M[Author]">Maschietto M</a></td>

</tr>

<tr valign="top"><td nowrap="">Citation(s)</td>

<td><span class="pubmed_id" id="39567898"><!--?xml version="1.0" encoding="UTF-8"?-->

<div class="PubmedCitation"><ul><li><span class="authors">Silva FLT, Euzébio MF, Ruas JS, Franco MT et al. </span><span class="title">Classification of pediatric soft and bone sarcomas using DNA methylation-based profiling. </span><span class="source">BMC Cancer</span> 2024 Nov 20;24(1):1428. PMID:&nbsp;<a title="Link to PubMed record" href="https://www.ncbi.nlm.nih.gov/pubmed/39567898">39567898</a></li></ul></div>

</span></td>

</tr>

<tr valign="top"><td colspan="2"><span id="geo2r"></span> <span id="rnaseq_counts"></span></td></tr>

<tr bgcolor="#eeeeee" valign="top"><td>Submission date</td>

<td>Aug 19, 2024</td>

</tr>

<tr bgcolor="#eeeeee" valign="top"><td>Last update date</td>

<td>Feb 04, 2025</td>

</tr>

<tr bgcolor="#eeeeee" valign="top"><td>Contact name</td>

<td>Felipe Silva</td>

</tr>

<tr bgcolor="#eeeeee" valign="top"><td nowrap="">E-mail(s)</td>

<td><a href="mailto:felipeluztorres@outlook.com">felipeluztorres@outlook.com</a><br></td>

</tr>

<tr bgcolor="#eeeeee" valign="top"><td nowrap="">Organization name</td>

<td style="text-align: justify">Boldrini<br></td>

</tr>

<tr bgcolor="#eeeeee" valign="top"><td nowrap="">Street address</td>

<td style="text-align: justify">R. Márcia Mendes, 506<br></td>

</tr>

<tr bgcolor="#eeeeee" valign="top"><td nowrap="">City</td>

<td style="text-align: justify">Campinas</td>

</tr>

<tr bgcolor="#eeeeee" valign="top"><td nowrap="">ZIP/Postal code</td>

<td style="text-align: justify">13083-884</td>

</tr>

<tr bgcolor="#eeeeee" valign="top"><td nowrap="">Country</td>

<td style="text-align: justify">Brazil</td>

</tr>

<tr valign="top"><td nowrap="">&nbsp;</td>

<td></td>

</tr>

<tr valign="top"><td>Platforms (2)</td>

<td onmouseout="onLinkOut('HelpMessage' , geo_empty_help)" onmouseover="onLinkOver('HelpMessage' , geoaxema_recenter)"><table cellpadding="3" style="position:relative;top:-5px;left:-5px"><tbody><tr><td valign="top"><a href="/geo/query/acc.cgi?acc=GPL21697" onmouseout="onLinkOut('HelpMessage' , geo_empty_help)" onmouseover="onLinkOver('HelpMessage' , geoaxema_recenter)">GPL21697</a></td>

<td valign="top">NextSeq 550 (Homo sapiens)</td>

</tr>

<tr><td valign="top"><a href="/geo/query/acc.cgi?acc=GPL34281" onmouseout="onLinkOut('HelpMessage' , geo_empty_help)" onmouseover="onLinkOver('HelpMessage' , geoaxema_recenter)">GPL34281</a></td>

<td valign="top">Illumina NovaSeq X (Homo sapiens)</td>

</tr>

</tbody></table></td>

</tr>

</td></tr></tbody></table>