<?xml version="1.0" encoding="UTF-8"?>
<EXPERIMENT_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <EXPERIMENT accession="SRX2409398" alias="Peds015_p15">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX2409398</PRIMARY_ID>
      <SUBMITTER_ID namespace="BI">Peds015_p15</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>RNA-Seq of a patient-derived tumor cell line: pediatric undifferentiated sarcoma</TITLE>
    <STUDY_REF accession="SRP078093">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP078093</PRIMARY_ID>
        <EXTERNAL_ID namespace="dbGaP">phs001121</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>To construct the RNA sequencing library, we isolated RNA from tissue or cell line samples and selected for poly(A)-enriched RNA. The RNA was fragmented, treated with DNase, and dephosphorylated. These RNA fragments were purified and the sample underwent RNA hydrolysis, ssDNA adapter ligation to the 3' end, followed by PCR enrichment. We then size selected the RNA molecules and sequenced them on a HiSeq 2500.</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS1546381" refcenter="phs001121" refname="CLF-PED-015-T">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS1546381</PRIMARY_ID>
          <SUBMITTER_ID namespace="phs001121">CLF-PED-015-T</SUBMITTER_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Peds015_p15</LIBRARY_NAME>
        <LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>TRANSCRIPTOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>other</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>204</SPOT_LENGTH>
          <READ_SPEC>
            <READ_INDEX>0</READ_INDEX>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Forward</READ_TYPE>
            <BASE_COORD>1</BASE_COORD>
          </READ_SPEC>
          <READ_SPEC>
            <READ_INDEX>1</READ_INDEX>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Reverse</READ_TYPE>
            <BASE_COORD>103</BASE_COORD>
          </READ_SPEC>
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 2500</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>alignment_software</TAG>
        <VALUE>TopHat v1.4.1</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
</EXPERIMENT_SET>
