ega-metadata-schema/examples/sequence-based-metadata/XML/XMLs_examples-true_values/experiment_IlluminaPaired.xml at main · EbiEga/ega-metadata-schema · GitHub

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<?xml version='1.0' encoding='UTF-8'?>
<EXPERIMENT_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_6/SRA.experiment.xsd">
  <EXPERIMENT alias="Example!_BM_15day_Africa-RG50002" center_name="GEO" broker_name="EGA">
    <TITLE>Example!_Illumina sequencing of Human RG50002 - 15 day treatment</TITLE>
    <STUDY_REF refname="Human Microbiome Project SP56J" refcenter="EBI-TEST"/>
    <DESIGN>
      <DESIGN_DESCRIPTION>Whole genome sequencing  - genomic library</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS001987"/>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Solexa-32824</LIBRARY_NAME>
        <LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED NOMINAL_LENGTH="260" NOMINAL_SDEV="50"/>
        </LIBRARY_LAYOUT>
        <TARGETED_LOCI>
          <LOCUS locus_name="other" description="ITS2; nuclear rRNA"/>
        </TARGETED_LOCI>
        <LIBRARY_CONSTRUCTION_PROTOCOL>Standard Illumina paired-end library construction protocol. Purified DNA was randomly fragmented using nebulisation and fraction was obtained by gel electrophoresis.</LIBRARY_CONSTRUCTION_PROTOCOL>
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>102</SPOT_LENGTH>
          <READ_SPEC>
            <READ_INDEX>0</READ_INDEX>
            <READ_LABEL>Forward_read</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</READ_LABEL>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Reverse</READ_TYPE>
            <BASE_COORD>55</BASE_COORD>
          </READ_SPEC>
          <READ_SPEC>
            <READ_INDEX>2</READ_INDEX>
            <READ_LABEL>barcode</READ_LABEL>
            <READ_CLASS>Technical Read</READ_CLASS>
            <READ_TYPE>BarCode</READ_TYPE>
            <EXPECTED_BASECALL_TABLE default_length="4">
              <BASECALL min_match="4" match_edge="full">TCAG</BASECALL>
            </EXPECTED_BASECALL_TABLE>
          </READ_SPEC>
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina Genome Analyzer</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
    <PROCESSING>
      <PIPELINE>
        <PIPE_SECTION>
          <STEP_INDEX>1</STEP_INDEX>
          <PREV_STEP_INDEX>NIL</PREV_STEP_INDEX>
          <PROGRAM>Rig Software</PROGRAM>
          <VERSION>2.3.306</VERSION>
          <NOTES>Image Analysis 1.3.4 - set birghtness to 30% through command X</NOTES>
        </PIPE_SECTION>
        <PIPE_SECTION>
          <STEP_INDEX>2</STEP_INDEX>
          <PREV_STEP_INDEX>1</PREV_STEP_INDEX>
          <PROGRAM>GAPipeline</PROGRAM>
          <VERSION>1.3.4</VERSION>
          <NOTES>Base calling programm - Command X</NOTES>
        </PIPE_SECTION>
      </PIPELINE>
    </PROCESSING>
    <EXPERIMENT_ATTRIBUTES>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>Forward Primer</TAG>
        <VALUE>GCCTTGCCAGCCCGATCAGTGAGAGTTTGATCCTGGCTCAG</VALUE>
      </EXPERIMENT_ATTRIBUTE>
      <EXPERIMENT_ATTRIBUTE>
        <TAG>Reverse Primer</TAG>
        <VALUE>GCCTTGCCAGCCCGATAAGAGAGAGTTTGATCCTGGCTCAG</VALUE>
      </EXPERIMENT_ATTRIBUTE>
    </EXPERIMENT_ATTRIBUTES>
  </EXPERIMENT>
</EXPERIMENT_SET>