<?xml version="1.0" encoding="UTF-8"?>
<EXPERIMENT_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <EXPERIMENT accession="SRX270695" center_name="BI" alias="1728661.WR33111.Solexa-126882.C1A4BACXX121109.P">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX270695</PRIMARY_ID>
      <SUBMITTER_ID namespace="BI">1728661.WR33111.Solexa-126882.C1A4BACXX121109.P</SUBMITTER_ID>
      <UUID>4ecf73e5-1a4c-4d24-b74c-1e7d53aed1d7</UUID>
    </IDENTIFIERS>
    <TITLE>Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-126882' containing sample 'Mycobacterium tuberculosis TKK-01-0017'</TITLE>
    <STUDY_REF accession="SRP021245">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP021245</PRIMARY_ID>
        <EXTERNAL_ID namespace="bioproject">PRJNA183515</EXTERNAL_ID>
        <EXTERNAL_ID namespace="Broad Institute" label="Mycobacterium tuberculosis TKK-01-0017">Mycobacterium tuberculosis TKK_01_0017_ltp_G059_WGS_Monoisolate</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>3-5 kb jumping library</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS415174">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS415174</PRIMARY_ID>
          <EXTERNAL_ID namespace="biosample">SAMN01828243</EXTERNAL_ID>
          <EXTERNAL_ID namespace="Broad Institute">Mycobacterium tuberculosis TKK-01-0017</EXTERNAL_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Solexa-126882</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED NOMINAL_LENGTH="479" NOMINAL_SDEV="200.82255"/>
        </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>2012-11-19 15:17:33.0</STEP_INDEX>
          <PREV_STEP_INDEX>N/A</PREV_STEP_INDEX>
          <PROGRAM>GAPipeline</PROGRAM>
          <VERSION>RTA1.15.19.5</VERSION>
          <NOTES>Sequencer Application 1.6.8.6</NOTES>
        </PIPE_SECTION>
      </PIPELINE>
    </PROCESSING>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>gssr_id</TAG>
        <VALUE>251357.0</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>lsid</TAG>
        <VALUE>broadinstitute.org:bsp.prod.sample:3MI96</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>material_type</TAG>
        <VALUE>DNA:DNA Somatic</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>project</TAG>
        <VALUE>G25257</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>root_sample_id</TAG>
        <VALUE>SM-332K9</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>sample_id</TAG>
        <VALUE>SM-3MI96</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>work_request</TAG>
        <VALUE>33111</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
  <EXPERIMENT accession="SRX270720" center_name="BI" alias="1728661.WR34332.Solexa-138717.D1NYDACXX130219.P">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX270720</PRIMARY_ID>
      <SUBMITTER_ID namespace="BI">1728661.WR34332.Solexa-138717.D1NYDACXX130219.P</SUBMITTER_ID>
      <UUID>8468904d-e1df-41c9-8f97-53d1adb7482c</UUID>
    </IDENTIFIERS>
    <TITLE>Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-138717' containing sample 'Mycobacterium tuberculosis TKK-01-0017' from individual 'TKK-01-0017'</TITLE>
    <STUDY_REF accession="SRP021245">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP021245</PRIMARY_ID>
        <EXTERNAL_ID namespace="bioproject">PRJNA183515</EXTERNAL_ID>
        <EXTERNAL_ID namespace="Broad Institute" label="Mycobacterium tuberculosis TKK-01-0017">Mycobacterium tuberculosis TKK_01_0017_ltp_G059_WGS_Monoisolate</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>3-5kb jump</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS415174">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS415174</PRIMARY_ID>
          <EXTERNAL_ID namespace="biosample">SAMN01828243</EXTERNAL_ID>
          <EXTERNAL_ID namespace="Broad Institute">Mycobacterium tuberculosis TKK-01-0017</EXTERNAL_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Solexa-138717</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED NOMINAL_LENGTH="5000" NOMINAL_SDEV="200.40061"/>
        </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>2013-03-02 13:23:59.0</STEP_INDEX>
          <PREV_STEP_INDEX>N/A</PREV_STEP_INDEX>
          <PROGRAM>GAPipeline</PROGRAM>
          <VERSION>RTA1.15.19.5</VERSION>
          <NOTES>Sequencer Application 1.6.8.6</NOTES>
        </PIPE_SECTION>
      </PIPELINE>
    </PROCESSING>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>gssr_id</TAG>
        <VALUE>280527.0</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>lsid</TAG>
        <VALUE>broadinstitute.org:bsp.prod.sample:3SD4E</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>material_type</TAG>
        <VALUE>DNA:DNA Somatic</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>product_order</TAG>
        <VALUE>PDO-31</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>product_part_number</TAG>
        <VALUE>P-MCV-0001</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>project</TAG>
        <VALUE>G27627</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>research_project</TAG>
        <VALUE>RP-114</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>root_sample_id</TAG>
        <VALUE>SM-2Z9RC</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>sample_id</TAG>
        <VALUE>SM-3SD4E</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>work_request</TAG>
        <VALUE>34332</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
  <EXPERIMENT accession="SRX270726" center_name="BI" alias="1728661.WR33936.Solexa-133942.C1FBVACXX130129.P">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX270726</PRIMARY_ID>
      <SUBMITTER_ID namespace="BI">1728661.WR33936.Solexa-133942.C1FBVACXX130129.P</SUBMITTER_ID>
      <UUID>7795d760-a4e2-409e-86e2-dc53923e629f</UUID>
    </IDENTIFIERS>
    <TITLE>Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-133942' containing sample 'Mycobacterium tuberculosis TKK-01-0017' from individual 'TKK-01-0017'</TITLE>
    <STUDY_REF accession="SRP021245">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP021245</PRIMARY_ID>
        <EXTERNAL_ID namespace="bioproject">PRJNA183515</EXTERNAL_ID>
        <EXTERNAL_ID namespace="Broad Institute" label="Mycobacterium tuberculosis TKK-01-0017">Mycobacterium tuberculosis TKK_01_0017_ltp_G059_WGS_Monoisolate</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>Illumina sequencing of Mycobacterium tuberculosis TKK-01-0017 via random selection</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS415174">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS415174</PRIMARY_ID>
          <EXTERNAL_ID namespace="biosample">SAMN01828243</EXTERNAL_ID>
          <EXTERNAL_ID namespace="Broad Institute">Mycobacterium tuberculosis TKK-01-0017</EXTERNAL_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Solexa-133942</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED NOMINAL_LENGTH="180" NOMINAL_SDEV="68.31888"/>
        </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>2013-02-10 17:29:11.0</STEP_INDEX>
          <PREV_STEP_INDEX>N/A</PREV_STEP_INDEX>
          <PROGRAM>GAPipeline</PROGRAM>
          <VERSION>RTA1.13.48</VERSION>
          <NOTES>Sequencer Application 1.5.15.1</NOTES>
        </PIPE_SECTION>
      </PIPELINE>
    </PROCESSING>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>gssr_id</TAG>
        <VALUE>274113.0</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>lsid</TAG>
        <VALUE>broadinstitute.org:bsp.prod.sample:3QQAJ</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>material_type</TAG>
        <VALUE>DNA:DNA Somatic</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>product_order</TAG>
        <VALUE>PDO-31</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>product_part_number</TAG>
        <VALUE>P-MCV-0001</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>project</TAG>
        <VALUE>G27627</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>research_project</TAG>
        <VALUE>RP-114</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>root_sample_id</TAG>
        <VALUE>SM-2Z9RC</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>sample_id</TAG>
        <VALUE>SM-3QQAJ</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>work_request</TAG>
        <VALUE>33936</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
  <EXPERIMENT accession="SRX270730" center_name="BI" alias="1728661.WR33155.Solexa-125083.D1CLVACXX121106.P">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX270730</PRIMARY_ID>
      <SUBMITTER_ID namespace="BI">1728661.WR33155.Solexa-125083.D1CLVACXX121106.P</SUBMITTER_ID>
      <UUID>f142bbcf-cc71-4758-a906-d5daf9300e61</UUID>
    </IDENTIFIERS>
    <TITLE>Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-125083' containing sample 'Mycobacterium tuberculosis TKK-01-0017'</TITLE>
    <STUDY_REF accession="SRP021245">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP021245</PRIMARY_ID>
        <EXTERNAL_ID namespace="bioproject">PRJNA183515</EXTERNAL_ID>
        <EXTERNAL_ID namespace="Broad Institute" label="Mycobacterium tuberculosis TKK-01-0017">Mycobacterium tuberculosis TKK_01_0017_ltp_G059_WGS_Monoisolate</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>Illumina sequencing of Mycobacterium tuberculosis TKK-01-0017 via random selection</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS415174">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS415174</PRIMARY_ID>
          <EXTERNAL_ID namespace="biosample">SAMN01828243</EXTERNAL_ID>
          <EXTERNAL_ID namespace="Broad Institute">Mycobacterium tuberculosis TKK-01-0017</EXTERNAL_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Solexa-125083</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED NOMINAL_LENGTH="200" NOMINAL_SDEV="72.17057"/>
        </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>2012-11-17 12:41:21.0</STEP_INDEX>
          <PREV_STEP_INDEX>N/A</PREV_STEP_INDEX>
          <PROGRAM>GAPipeline</PROGRAM>
          <VERSION>RTA1.15.19.5</VERSION>
          <NOTES>Sequencer Application 1.6.8.6</NOTES>
        </PIPE_SECTION>
      </PIPELINE>
    </PROCESSING>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>gssr_id</TAG>
        <VALUE>251617.0</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>lsid</TAG>
        <VALUE>broadinstitute.org:bsp.prod.sample:3MJND</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>material_type</TAG>
        <VALUE>DNA:DNA Somatic</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>project</TAG>
        <VALUE>G25257</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>root_sample_id</TAG>
        <VALUE>SM-332K9</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>sample_id</TAG>
        <VALUE>SM-3MJND</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>work_request</TAG>
        <VALUE>33155</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
</EXPERIMENT_SET>
