<?xml version="1.0" encoding="UTF-8"?>
<EXPERIMENT_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <EXPERIMENT accession="SRX473395" center_name="BI" alias="2838348.WR39953.Pond-322018.C3UMYACXX140212.P">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX473395</PRIMARY_ID>
      <SUBMITTER_ID namespace="BI">2838348.WR39953.Pond-322018.C3UMYACXX140212.P</SUBMITTER_ID>
      <UUID>bd3ca893-f13b-4d8c-a1eb-1c8e929f213a</UUID>
    </IDENTIFIERS>
    <TITLE>Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Pond-322018' containing sample 'TKK_05MA_0054' from individual '023-06-0054'</TITLE>
    <STUDY_REF accession="SRP038421">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP038421</PRIMARY_ID>
        <EXTERNAL_ID namespace="bioproject">PRJNA235523</EXTERNAL_ID>
        <EXTERNAL_ID namespace="Broad Institute" label="Mycobacterium tuberculosis TKK_05MA_0054">TB ARC KRITH 2 Mycobacterium_tuberculosis_TKK_05MA_0054_ltp_AM40_WGS_Monoisolate</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>Illumina sequencing of Mycobacterium tuberculosis TKK_05MA_0054 via random selection</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS559718">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS559718</PRIMARY_ID>
          <EXTERNAL_ID namespace="biosample">SAMN02586013</EXTERNAL_ID>
          <EXTERNAL_ID namespace="Broad Institute">TKK_05MA_0054</EXTERNAL_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Pond-322018</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED NOMINAL_SDEV="114.78534" NOMINAL_LENGTH="180"/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>202</SPOT_LENGTH>
          <READ_SPEC>
            <READ_INDEX>0</READ_INDEX>
            <READ_LABEL>forward</READ_LABEL>
            <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_LABEL>reverse</READ_LABEL>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Reverse</READ_TYPE>
            <BASE_COORD>102</BASE_COORD>
          </READ_SPEC>
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 2000</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
    <PROCESSING>
      <PIPELINE>
        <PIPE_SECTION section_name="base caller">
          <STEP_INDEX>2014-02-18 13:26:54.0</STEP_INDEX>
          <PREV_STEP_INDEX>N/A</PREV_STEP_INDEX>
          <PROGRAM>GAPipeline</PROGRAM>
          <VERSION>RTA1.17.21.3</VERSION>
          <NOTES>Sequencer Application 2.1.35.0</NOTES>
        </PIPE_SECTION>
      </PIPELINE>
    </PROCESSING>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>analysis_type</TAG>
        <VALUE>AssemblyWithReference</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>data_type</TAG>
        <VALUE>WGS</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>gssr_id</TAG>
        <VALUE>482959.0</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>library_type</TAG>
        <VALUE>IlluminaStufferlessJump</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>lsid</TAG>
        <VALUE>broadinstitute.org:bsp.prod.sample:5FSRP</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>material_type</TAG>
        <VALUE>DNA:DNA Somatic</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>product_order</TAG>
        <VALUE>PDO-3213</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>product_part_number</TAG>
        <VALUE>P-WG-0033</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>project</TAG>
        <VALUE>G58172</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>research_project</TAG>
        <VALUE>RP-114</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>root_sample_id</TAG>
        <VALUE>SM-4Q742</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>sample_id</TAG>
        <VALUE>SM-5FSRP</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>work_request</TAG>
        <VALUE>39953</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
  <EXPERIMENT accession="SRX481814" center_name="BI" alias="2838348.WR39953.Pond-322018.H7H4FADXX140301.P">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX481814</PRIMARY_ID>
      <SUBMITTER_ID namespace="BI">2838348.WR39953.Pond-322018.H7H4FADXX140301.P</SUBMITTER_ID>
      <UUID>b0441052-97c0-42c9-aa2d-fb7880a04a49</UUID>
    </IDENTIFIERS>
    <TITLE>Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Pond-322018' containing sample 'TKK_05MA_0054' from individual '023-06-0054'</TITLE>
    <STUDY_REF accession="SRP038421">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP038421</PRIMARY_ID>
        <EXTERNAL_ID namespace="bioproject">PRJNA235523</EXTERNAL_ID>
        <EXTERNAL_ID namespace="Broad Institute" label="Mycobacterium tuberculosis TKK_05MA_0054">TB ARC KRITH 2 Mycobacterium_tuberculosis_TKK_05MA_0054_ltp_AM40_WGS_Monoisolate</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>Illumina sequencing of Mycobacterium tuberculosis TKK_05MA_0054 via random selection</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS559718">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS559718</PRIMARY_ID>
          <EXTERNAL_ID namespace="biosample">SAMN02586013</EXTERNAL_ID>
          <EXTERNAL_ID namespace="Broad Institute">TKK_05MA_0054</EXTERNAL_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Pond-322018</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED NOMINAL_SDEV="106.01865" NOMINAL_LENGTH="180"/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>202</SPOT_LENGTH>
          <READ_SPEC>
            <READ_INDEX>0</READ_INDEX>
            <READ_LABEL>forward</READ_LABEL>
            <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_LABEL>reverse</READ_LABEL>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Reverse</READ_TYPE>
            <BASE_COORD>102</BASE_COORD>
          </READ_SPEC>
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 2000</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
    <PROCESSING>
      <PIPELINE>
        <PIPE_SECTION section_name="base caller">
          <STEP_INDEX>2014-03-02 13:48:29.0</STEP_INDEX>
          <PREV_STEP_INDEX>N/A</PREV_STEP_INDEX>
          <PROGRAM>GAPipeline</PROGRAM>
          <VERSION>RTA1.17.21.3</VERSION>
          <NOTES>Sequencer Application 2.0.12.0</NOTES>
        </PIPE_SECTION>
      </PIPELINE>
    </PROCESSING>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>analysis_type</TAG>
        <VALUE>AssemblyWithReference</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>data_type</TAG>
        <VALUE>WGS</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>gssr_id</TAG>
        <VALUE>482959.0</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>library_type</TAG>
        <VALUE>WholeGenomeShotgun</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>lsid</TAG>
        <VALUE>broadinstitute.org:bsp.prod.sample:5FSRP</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>material_type</TAG>
        <VALUE>DNA:DNA Somatic</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>product_order</TAG>
        <VALUE>PDO-3213</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>product_part_number</TAG>
        <VALUE>P-WG-0033</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>project</TAG>
        <VALUE>G58172</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>research_project</TAG>
        <VALUE>RP-114</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>root_sample_id</TAG>
        <VALUE>SM-4Q742</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>sample_id</TAG>
        <VALUE>SM-5FSRP</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>work_request</TAG>
        <VALUE>39953</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
  <EXPERIMENT accession="SRX493557" center_name="BI" alias="2838348.WR39953.Pond-322018.C37KUACXX140306.P">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX493557</PRIMARY_ID>
      <SUBMITTER_ID namespace="BI">2838348.WR39953.Pond-322018.C37KUACXX140306.P</SUBMITTER_ID>
      <UUID>afca8bce-60a0-44e8-aaad-ef9ba75a9b13</UUID>
    </IDENTIFIERS>
    <TITLE>Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Pond-322018' containing sample 'TKK_05MA_0054' from individual '023-06-0054'</TITLE>
    <STUDY_REF accession="SRP038421">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP038421</PRIMARY_ID>
        <EXTERNAL_ID namespace="bioproject">PRJNA235523</EXTERNAL_ID>
        <EXTERNAL_ID namespace="Broad Institute" label="Mycobacterium tuberculosis TKK_05MA_0054">TB ARC KRITH 2 Mycobacterium_tuberculosis_TKK_05MA_0054_ltp_AM40_WGS_Monoisolate</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>Illumina sequencing of Mycobacterium tuberculosis TKK_05MA_0054 via random selection</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS559718">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS559718</PRIMARY_ID>
          <EXTERNAL_ID namespace="biosample">SAMN02586013</EXTERNAL_ID>
          <EXTERNAL_ID namespace="Broad Institute">TKK_05MA_0054</EXTERNAL_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Pond-322018</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED NOMINAL_SDEV="107.1534775" NOMINAL_LENGTH="180"/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>202</SPOT_LENGTH>
          <READ_SPEC>
            <READ_INDEX>0</READ_INDEX>
            <READ_LABEL>forward</READ_LABEL>
            <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_LABEL>reverse</READ_LABEL>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Reverse</READ_TYPE>
            <BASE_COORD>102</BASE_COORD>
          </READ_SPEC>
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 2000</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
    <PROCESSING>
      <PIPELINE>
        <PIPE_SECTION section_name="base caller">
          <STEP_INDEX>2014-03-11 22:50:56.0</STEP_INDEX>
          <PREV_STEP_INDEX>N/A</PREV_STEP_INDEX>
          <PROGRAM>GAPipeline</PROGRAM>
          <VERSION>RTA1.17.21.3</VERSION>
          <NOTES>Sequencer Application 2.1.35.0</NOTES>
        </PIPE_SECTION>
      </PIPELINE>
    </PROCESSING>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>analysis_type</TAG>
        <VALUE>AssemblyWithReference</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>data_type</TAG>
        <VALUE>WGS</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>gssr_id</TAG>
        <VALUE>482959.0</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>library_type</TAG>
        <VALUE>WholeGenomeShotgun</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>lsid</TAG>
        <VALUE>broadinstitute.org:bsp.prod.sample:5FSRP</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>material_type</TAG>
        <VALUE>DNA:DNA Somatic</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>product_order</TAG>
        <VALUE>PDO-3213</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>product_part_number</TAG>
        <VALUE>P-WG-0033</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>project</TAG>
        <VALUE>G58172</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>research_project</TAG>
        <VALUE>RP-114</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>root_sample_id</TAG>
        <VALUE>SM-4Q742</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>sample_id</TAG>
        <VALUE>SM-5FSRP</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>work_request</TAG>
        <VALUE>39953</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
</EXPERIMENT_SET>
