<?xml version="1.0" encoding="UTF-8"?>
<EXPERIMENT_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <EXPERIMENT accession="SRX079626" center_name="BI" alias="215369.WR24804.Pond-61916.B084DABXX110425.tagged_332.P">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX079626</PRIMARY_ID>
      <SUBMITTER_ID namespace="BI">215369.WR24804.Pond-61916.B084DABXX110425.tagged_332.P</SUBMITTER_ID>
      <UUID>25f61d33-a056-49a7-8f99-12eb872a2ab7</UUID>
    </IDENTIFIERS>
    <TITLE>Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Pond-61916' containing sample 'Treponema denticola'</TITLE>
    <STUDY_REF accession="SRP006301">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP006301</PRIMARY_ID>
        <EXTERNAL_ID namespace="bioproject">PRJNA64913</EXTERNAL_ID>
        <EXTERNAL_ID namespace="Broad Institute" label="Treponema denticola H1-T">Reference genome for the Human Microbiome Project Treponema_denticola_H1_T_ltp_HMPREF9725_WGS_Monoisolate</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>low coverage of genome on Illumina</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS184242">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS184242</PRIMARY_ID>
          <SUBMITTER_ID namespace="BI">PRJNA28331.Treponema denticola</SUBMITTER_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Pond-61916</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED NOMINAL_LENGTH="96" NOMINAL_SDEV="21.52863"/>
        </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">CACATCCT</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>2011-05-05 13:32:34.0</STEP_INDEX>
          <PREV_STEP_INDEX>N/A</PREV_STEP_INDEX>
          <PROGRAM>GAPipeline</PROGRAM>
          <VERSION>RTA1.10.36</VERSION>
          <NOTES>Sequencer Application 1.3.8</NOTES>
        </PIPE_SECTION>
      </PIPELINE>
    </PROCESSING>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>gssr_id</TAG>
        <VALUE>65742.1</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>lsid</TAG>
        <VALUE>BROAD:SEQUENCING_SAMPLE:65742.1</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>material_type</TAG>
        <VALUE>Genomic DNA</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>project</TAG>
        <VALUE>G10810</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>work_request</TAG>
        <VALUE>24804</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
</EXPERIMENT_SET>
