<?xml version="1.0" encoding="UTF-8"?>
<EXPERIMENT_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <EXPERIMENT accession="SRX115179" center_name="BI" alias="385303.WR26384.Solexa-73501.D0ENAACXX111117.P">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX115179</PRIMARY_ID>
      <SUBMITTER_ID namespace="BI">385303.WR26384.Solexa-73501.D0ENAACXX111117.P</SUBMITTER_ID>
      <UUID>2c269ceb-04dc-4295-bab9-344389d12c9a</UUID>
    </IDENTIFIERS>
    <TITLE>Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-73501' containing sample 'Clostridium clostridioforme 90A1'</TITLE>
    <STUDY_REF accession="SRP010209">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP010209</PRIMARY_ID>
        <EXTERNAL_ID namespace="bioproject">PRJNA64857</EXTERNAL_ID>
        <EXTERNAL_ID namespace="Broad Institute" label="Clostridium clostridioforme 90A1">Reference genome for the Human Microbiome Project Clostridium_clostridioforme_90A1_ltp_HMPREF1087_WGS_Monoisolate</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>3-5kb jumps on Illumina</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS285456">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS285456</PRIMARY_ID>
          <SUBMITTER_ID namespace="BI">PRJNA28331.Clostridium clostridioforme 90A1</SUBMITTER_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Solexa-73501</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED NOMINAL_LENGTH="531" NOMINAL_SDEV="128.0743"/>
        </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>2011-11-28 23:49:04.0</STEP_INDEX>
          <PREV_STEP_INDEX>N/A</PREV_STEP_INDEX>
          <PROGRAM>GAPipeline</PROGRAM>
          <VERSION>RTA1.12.4.2</VERSION>
          <NOTES>Sequencer Application 1.4.8</NOTES>
        </PIPE_SECTION>
      </PIPELINE>
    </PROCESSING>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>gssr_id</TAG>
        <VALUE>108307.0</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>lsid</TAG>
        <VALUE>broadinstitute.org:bsp.prod.sample:21SU1</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>material_type</TAG>
        <VALUE>DNA:DNA Somatic</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>project</TAG>
        <VALUE>G14148</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>root_sample_id</TAG>
        <VALUE>SM-1VO19</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>sample_id</TAG>
        <VALUE>SM-21SU1</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>work_request</TAG>
        <VALUE>26384</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
  <EXPERIMENT accession="SRX115885" center_name="BI" alias="385303.WR25825.Pond-75836.B028JACXX110725.tagged_117.P">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX115885</PRIMARY_ID>
      <SUBMITTER_ID namespace="BI">385303.WR25825.Pond-75836.B028JACXX110725.tagged_117.P</SUBMITTER_ID>
      <UUID>0bbcb3bf-820a-488f-a38c-629f1f7e745a</UUID>
    </IDENTIFIERS>
    <TITLE>Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Pond-75836' containing sample 'Clostridium clostridioforme 90A1'</TITLE>
    <STUDY_REF accession="SRP010209">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP010209</PRIMARY_ID>
        <EXTERNAL_ID namespace="bioproject">PRJNA64857</EXTERNAL_ID>
        <EXTERNAL_ID namespace="Broad Institute" label="Clostridium clostridioforme 90A1">Reference genome for the Human Microbiome Project Clostridium_clostridioforme_90A1_ltp_HMPREF1087_WGS_Monoisolate</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>Illumina sequencing of Clostridium clostridioforme 90A1 via random selection</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS285456">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS285456</PRIMARY_ID>
          <SUBMITTER_ID namespace="BI">PRJNA28331.Clostridium clostridioforme 90A1</SUBMITTER_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Pond-75836</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED NOMINAL_LENGTH="310" NOMINAL_SDEV="14.1336"/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>210</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>barcode</READ_LABEL>
            <READ_CLASS>Technical Read</READ_CLASS>
            <READ_TYPE>BarCode</READ_TYPE>
            <EXPECTED_BASECALL_TABLE default_length="8" base_coord="102">
              <BASECALL min_match="7" max_mismatch="1" match_edge="full">ACCAACTG</BASECALL>
            </EXPECTED_BASECALL_TABLE>
          </READ_SPEC>
          <READ_SPEC>
            <READ_INDEX>2</READ_INDEX>
            <READ_LABEL>reverse</READ_LABEL>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Reverse</READ_TYPE>
            <BASE_COORD>110</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>2011-08-06 13:26:27.0</STEP_INDEX>
          <PREV_STEP_INDEX>N/A</PREV_STEP_INDEX>
          <PROGRAM>GAPipeline</PROGRAM>
          <VERSION>RTA1.12.4.2</VERSION>
          <NOTES>Sequencer Application 1.4.8</NOTES>
        </PIPE_SECTION>
      </PIPELINE>
    </PROCESSING>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>gssr_id</TAG>
        <VALUE>108289.0</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>lsid</TAG>
        <VALUE>broadinstitute.org:bsp.prod.sample:21SQ9</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>material_type</TAG>
        <VALUE>DNA:DNA Somatic</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>project</TAG>
        <VALUE>G14148</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>root_sample_id</TAG>
        <VALUE>SM-1VO19</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>sample_id</TAG>
        <VALUE>SM-21SQ9</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>work_request</TAG>
        <VALUE>25825</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
  <EXPERIMENT accession="SRX184881" center_name="BI" alias="385303.WR31480.Solexa-110985.C0W0UACXX120807.P">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX184881</PRIMARY_ID>
      <SUBMITTER_ID namespace="BI">385303.WR31480.Solexa-110985.C0W0UACXX120807.P</SUBMITTER_ID>
      <UUID>2f3d1d71-28fe-4325-888e-66c117f6c083</UUID>
    </IDENTIFIERS>
    <TITLE>Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-110985' containing sample 'Clostridium clostridioforme 90A1'</TITLE>
    <STUDY_REF accession="SRP010209">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP010209</PRIMARY_ID>
        <EXTERNAL_ID namespace="bioproject">PRJNA64857</EXTERNAL_ID>
        <EXTERNAL_ID namespace="Broad Institute" label="Clostridium clostridioforme 90A1">Reference genome for the Human Microbiome Project Clostridium_clostridioforme_90A1_ltp_HMPREF1087_WGS_Monoisolate</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>3-5 kb jumps</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS285456">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS285456</PRIMARY_ID>
          <SUBMITTER_ID namespace="BI">PRJNA28331.Clostridium clostridioforme 90A1</SUBMITTER_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Solexa-110985</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED NOMINAL_LENGTH="4000" NOMINAL_SDEV="186.66324"/>
        </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>2012-08-21 14:21:58.0</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>analysis_type</TAG>
        <VALUE>AssemblyWithReference</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>gssr_id</TAG>
        <VALUE>209839.0</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:39R37</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>material_type</TAG>
        <VALUE>DNA:DNA Somatic</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>project</TAG>
        <VALUE>G14148</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>root_sample_id</TAG>
        <VALUE>SM-1VO19</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>sample_id</TAG>
        <VALUE>SM-39R37</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>work_request</TAG>
        <VALUE>31480</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
</EXPERIMENT_SET>
