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<EXPERIMENT_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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      <PRIMARY_ID>SRX24274108</PRIMARY_ID>
      <SUBMITTER_ID namespace="NCI-phs003586">ATID582_WES</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>Whole exome sequencing on triple negative breast cancer tumor.</TITLE>
    <STUDY_REF accession="SRP504603">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP504603</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioProject">PRJNA1087012</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>DNA was shared by sonication using Covaris E220 and library prepared using the KAPA library prep kit with the "with beads" protocol.  Exomes were captured using Roche Nimblegen Exome V3 kits.</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS21040074" refname="ATID582_WES" refcenter="phs003586">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS21040074</PRIMARY_ID>
          <SUBMITTER_ID namespace="phs003586">ATID582_WES</SUBMITTER_ID>
        </IDENTIFIERS>
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      <LIBRARY_DESCRIPTOR>
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        <LIBRARY_STRATEGY>WXS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina NovaSeq 6000</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>alignment_software</TAG>
        <VALUE>BWA</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
  <EXPERIMENT accession="SRX24274109" alias="ATID473_WES">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX24274109</PRIMARY_ID>
      <SUBMITTER_ID namespace="NCI-phs003586">ATID473_WES</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>Whole exome sequencing on triple negative breast cancer tumor.</TITLE>
    <STUDY_REF accession="SRP504603">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP504603</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioProject">PRJNA1087012</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>DNA was shared by sonication using Covaris E220 and library prepared using the KAPA library prep kit with the "with beads" protocol.  Exomes were captured using Roche Nimblegen Exome V3 kits.</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS21040076" refname="ATID473_WES" refcenter="phs003586">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS21040076</PRIMARY_ID>
          <SUBMITTER_ID namespace="phs003586">ATID473_WES</SUBMITTER_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>ATID473_WES</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WXS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>PCR</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina NovaSeq 6000</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>alignment_software</TAG>
        <VALUE>BWA</VALUE>
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    <IDENTIFIERS>
      <PRIMARY_ID>SRX24274110</PRIMARY_ID>
      <SUBMITTER_ID namespace="NCI-phs003586">ATID582_RNA</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>RNA-Seq on triple negative breast cancer tumor.</TITLE>
    <STUDY_REF accession="SRP504603">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP504603</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioProject">PRJNA1087012</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>Total RNA was extracted using the NORGEN Total RNA Purification Kit and treated with DNase I.  RNA was purified using the AMPure XP beads.  cDNA was prepared using the Ovation RNA-Seq System V2 and then shared using the Covaris E220 sonicator.  Library was prepared using the Agilent SureSelect XT Low Input Reagent Kit.  The libraries were then hybridized to Agilent SureSelect Human All Exon v.4 probes.</DESIGN_DESCRIPTION>
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        <IDENTIFIERS>
          <PRIMARY_ID>SRS21040075</PRIMARY_ID>
          <SUBMITTER_ID namespace="phs003586">ATID582_RNA</SUBMITTER_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>ATID582_RNA</LIBRARY_NAME>
        <LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>TRANSCRIPTOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>PolyA</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
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      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina NovaSeq 6000</INSTRUMENT_MODEL>
      </ILLUMINA>
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      <EXPERIMENT_ATTRIBUTE>
        <TAG>alignment_software</TAG>
        <VALUE>STAR</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
  <EXPERIMENT accession="SRX24274111" alias="ATID473_RNA">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX24274111</PRIMARY_ID>
      <SUBMITTER_ID namespace="NCI-phs003586">ATID473_RNA</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>RNA-Seq on triple negative breast cancer tumor.</TITLE>
    <STUDY_REF accession="SRP504603">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP504603</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioProject">PRJNA1087012</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>Total RNA was extracted using the NORGEN Total RNA Purification Kit and treated with DNase I.  RNA was purified using the AMPure XP beads.  cDNA was prepared using the Ovation RNA-Seq System V2 and then shared using the Covaris E220 sonicator.  Library was prepared using the Agilent SureSelect XT Low Input Reagent Kit.  The libraries were then hybridized to Agilent SureSelect Human All Exon v.4 probes.</DESIGN_DESCRIPTION>
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        <IDENTIFIERS>
          <PRIMARY_ID>SRS21040077</PRIMARY_ID>
          <SUBMITTER_ID namespace="phs003586">ATID473_RNA</SUBMITTER_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
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        <LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>TRANSCRIPTOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>PolyA</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina NovaSeq 6000</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>alignment_software</TAG>
        <VALUE>STAR</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
</EXPERIMENT_SET>
