<?xml version="1.0" encoding="UTF-8"?>
<!--$Id: gt_submission_in-wrong-subdir.xml,v 1.1 2003/12/03 18:19:32 mummi Exp $ -->
<assay_submission lsid="urn:lsid:dcc.hapmap.org:Batch:23432:1"
  xmlns="http://hapmap.cshl.org"
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
  xsi:schemaLocation="http://hapmap.cshl.org http://hapmap.cshl.org/xml-schema/2003-10-14/hapmap.xsd">
    <batch_info>
    <class>NEW</class>
    <date_created>2003-09-14</date_created>
    <contact>
      <name>mummi</name>
      <email>mummi@cshl.org</email>
    </contact>
    <comment> 
      This a test submission file that has valid XML and consistent assay data (i.e. oligos that actually are 
derived from the parent SNP  flanks. This file should pass the upload-processing tests, get imported
 into the tracking database, pass the consistency tests there an eventually get imported into the 
 main database. Last updated: $Date: 2003/12/03 18:19:32 $
     </comment>
  </batch_info>
  <assays>
    <!--Illumina's BeadArray platform (also used by Sanger and McGill/GQIC)-->
    <assay lsid="urn:lsid:illumina.hapmap.org:Assay:0034:1">
      <snp_assayed lsid="urn:LSID:ncbi.nlm.nih.gov:dbSNP/refSNP:rs1455353:88"/>
      <protocol_used lsid="urn:LSID:illumina.hapmap.org:Protocol:Golden_Gate_assay_design_1.0.0:1"/>
      <batch type="multiplex-pool">pool-13_2003-02-11</batch>
      <status>
        <pass/>
      </status>
      <input_parameters>
        <beadarray_platform>
          <seq_for_oligo_design>ATAGGCATATTCCCTGTGCTTCAGGATCCCGTCCAACAATAAGGACCCATTAACACACACACATGACAGACGCAACTGGCCAATTTTTTAAGTCTAATCTGAAAAGCATTCTTGATTGCC[C/T]GCTAGCATAAAGAATCCCCTTTAAACTCTGTATCAAACAAGACAATACCAAAAAGCTACTCATAAAATCATATATACTATTCAATTCCCAATATATATAAAATTAAATATGAAAA</seq_for_oligo_design>
        </beadarray_platform>
      </input_parameters>
      <output_design>
        <strand>forward</strand>
        <beadarray_platform>
          <allele1_combined_seq>ACTTCGTCAGTAACGGACTCTGAAAAGCATTCTTGATTGCCT</allele1_combined_seq>
          <allele2_combined_seq>GAGTCGAGGTCATATCGTTCTGAAAAGCATTCTTGATTGCCC</allele2_combined_seq>
          <common_combined_seq>CTAGCATAAAGAATCCCCTTTAACTCAATCTTTGCGAGACACGTCGGTCTGCCTATAGTGAGTC</common_combined_seq>
          <illumina_strand>bottom</illumina_strand>
        </beadarray_platform>
      </output_design>
    </assay>
    <!--IMSUT-Riken's Invader platform -->
    <assay lsid="urn:lsid:imsut-riken.hapmap.org:Assay:0035:1">
      <snp_assayed lsid="urn:lsid:ncbi.nlm.nih.gov:dbSNP/refSNP:rs100016:108"/>
      <protocol_used lsid="urn:LSID:imsut-riken.hapmap.org:Protocol:assay_design:1"/>
      <batch type="multiplex-pool">pool-13_2003-02-11</batch>
      <status>
        <pass/>
      </status>
      <input_parameters>
        <invader_platform>
          <seq_for_probe_design>GCTCACCTTCTCTCAATCTTTTCAGGGATCAGTTCTTTGCTCTTTGAAACGAGATGATCC[G/A]TCTCACACTGAAAGTTTCCTATCGTGAGGTTCAGTGTCATCTAGAGTCAACGGATGAAGT</seq_for_probe_design>
          <seq_for_primer_design>TCCTGCTGATCCCTGACTGGTCAGACTCCTCCTGTCATGACAACATACACTTAGGGATGGGGCATCTGCAGCCATGGAATGAGATTTCACTAGTTACCTGGGTTGTTGGTGCTAAGTGAATCAACCAGAAATGTAAGCAAATTTAATCTCAAGTACTTTTCTGCATGGGCAAGATGGGGCACGTGTTGATACTTATTTCTGGTAACACTGGTAGGAGTCTTTCCTATGAAAGTGTAATACAGAGAACGTAATACACTAGAGTTTGGGCCAAAAGAAAGAGACGACAATGACAACAATAATAACAACAAAACCCTCCGTAGTTACAGGGAAAACTTTTTTTGCTATTTTTTAATGGAAAAGGAACAGTTTCAATATTCAGTTTATCTTCTTTATCCAGCCTCTTCTTTTTGTGTTGTAGAAATTCCACAGTGAACACTTATACTTCATCCGTTGACTCTAGATGACACTGAACCTCACGATAGGAAACTTTCAGTGTGAGATGGATCATCTCGTTTCAAAGAGCAAAGAACTGATCCCTGAAAAGATTGAGAGAAGGTGAGCTTCCATTGATAAAAACCAGGAATACAGGTTTTTCATATTCTCCCAGCAAGTTAAATGTGGAAGTAGAATAATTTCTTCCAAAACAAGGAGACAAAGATATTGTTAATCCTTTCAATTGCATTACTTTTAGCAGCCGTAAAAATAAGCCCAGCAACAAATACTCAGGGTCTTAAATGAAAGCAGAGTAGATTTAAGAGAATTGGAGCGGAGGGCACAATGAAAGGCCCTTTGCCTTTCATTTTGAATTTTTTGTGTAGTCAGTTGTCCAGCGACTGTGACTCCATGAGGGAGGGTGGTCATCCCTGCACAGCTGCAAAGGGTAGGGGCCGTGATTTCCACCTCTTTTCCTCCCACGTCTCTGTCAATCTGGCTTCCACTGAAATCACTTTCACTAATGCACTAATAAATCCCCAACGGCTTAATCTACCTATCTAGGCTGT</seq_for_primer_design>
        </invader_platform>
      </input_parameters>
      <output_design>
        <strand>forward</strand>
        <invader_platform>
          <pcr_primer_forward>CCTGGGTTGTTGGTGCTAAG</pcr_primer_forward>
          <pcr_primer_reverse>TGGAAGCTCACCTTCTCTCAATC</pcr_primer_reverse>
          <invader_probe>TGACACTGAACCTCACGATAGGAAACTTTCAGTGTGAGAA</invader_probe>
          <allele_probe1>TGGATCATCTCGTTTCAAA</allele_probe1>
          <allele_probe2>CGGATCATCTCGTTTCAA</allele_probe2>
        </invader_platform>
      </output_design>
    </assay>
    <!--Whitehead's Sequenom platform -->
    <assay lsid="urn:lsid:wicgr.hapmap.org:Assay:0036:1">
      <snp_assayed lsid="urn:lsid:ncbi.nlm.nih.gov:dbSNP/refSNP:rs1528272:88"/>
      <protocol_used lsid="urn:lsid:wicgr.hapmap.org:Protocol:assay_design_1:1"/>
      <batch type="multiplex-pool">batch_2003-02-11</batch>
      <status>
        <pass/>
      </status>
      <input_parameters>
        <sequenom_platform>
          <seq_for_oligo_design>tgaaaNtgcctttgtaagactaatgaaaaatgacaagattaggctatgggaggtgcctttcatagcatgcctttctataattgtttactgcaccagaagtcacaagatttgtgactctcccaactgatcctatagataacatcatattgtagaatctaagattggtcttttgagatgtgtttcaaacctttgcattctagtgactgactgactccacctggatttgtgcctcatgattcagcccatcctgtggtcccatctagaggcagactcagctcatgcataaggatagttttccctatgatttaattccccaacgaatcagcagcacacattccctagccccactgcctgccaaccctagcctgtgagttctcagggaggctgatttgagtaataaactccatctacNacttggctagcaNtgcattaattaagctctttatttGCTaaatttcagttagttcagaggaataagttcaagagatctattgtacattatggtgattatagttaataacatatattgtataattgaaaattgctgagagtatattttaagtgcaaaatataagcatgtgaggtgattcatatgctaattagcttgatttagccagcccacaatgtatatatatatcataacatcatgctgtatctcatgaacatatacaatttttatctgtcaattaagaagaaTTAAAATAAATAAATCTGTAATTTCATTGACCATTTCTCACAGGTTGTTTTAAAGCATAAGTTAAGGTGATCAACATATTCTTCTCTTTGTTATACTTTTCCCTACTTGATATATTAGTGAGAATATTAATTATCACCTCATTCTCAATGACTAGGTTAATTACTACAATTATTTTAACTAATATAACTTTAAATACTACTNTAGAGTTTCTACTCTTAGTATGCTTTATTTGTGGATAAACACTTTTAGTTATCTAGGTACATTTTTATGGCACTTGGATTTGATGGGAATAAAAAGAAATTA[T/G]CCTGATCTAAATCTTTAGTCTTTCTTTGTATTCTCCATATATTAGTCATGGTTTCCATGTTGTTGAATTGTCCTTTTTTGGAGTTAACATGCCTGATTTCTGTTTACATTGGCCAATAAGAGGATGTAGAACTGCAGCTGGTATTTAATTCTAATTATTTGCATTTTTCAATAACATTTATTTCAGAAAAATTTTTCAAGATTATTTTTTGCTAAGCACAAGATATTTGCTATTCTGTACCATGTTCCCTAAAAGCATAATGCTAATAGAAATCTGCACCTTGattaatttttatattaaaaaaCAAGTggctaggcacagtggctcacatctgtaatcccaacactttgggaggctgaggtgggtgatcacttgaggtgaggagttcaagaccagcctagccaacatggtgaaaccctatctccactaaaaatacaaaaattagctgggcatggttgtgcacgcctgtaatcccGGGCAACAGAGCAAGACTCTGTTTCAAAAAACA</seq_for_oligo_design>
        </sequenom_platform>
      </input_parameters>
      <output_design>
        <strand>forward</strand>
        <sequenom_platform>
          <pcr_primer_forward>ATGGCACTTGGATTTGATGG</pcr_primer_forward>
          <pcr_primer_reverse>ACAACATGGAAACCATGACT</pcr_primer_reverse>
          <extension_probe>GAAAGACTAAAGATTTAGATCAGG</extension_probe>
        </sequenom_platform>
      </output_design>
    </assay>
    <!--UCSF/WU's FTP-TDI platform -->
    <assay lsid="urn:lsid:ucsf-wu.hapmap.org:Assay:rs003424:1">
      <snp_assayed lsid="urn:lsid:ncbi.nlm.nih.gov:dbSNP/refSNP:rs1024748:116.2"/>
      <protocol_used lsid="urn:lsid:ucsf-wu.hapmap.org:Protocol:assay_design:1"/>
      <batch type="multiplex-pool">batch_2003-02-11_ff</batch>
      <status>
        <pass/>
      </status>
      <input_parameters>
        <fp_tdi_platform>
          <seq_for_pcr_oligo_design>TATATGGTTATATTTCATTAATATATTCTAGTTTGTTCAGCTGTTCTTACTGGGTGAATTTGTGTGGTTTCCTGACATTTTTGTTTTTAGTAGTGCCTCAGTAGTTTTATACATAATTACGTTTCCCTTCTGGATTATTTCCTTAGTATCTAGTTCAAGAAGTGAAATCGCTGGATTCTTGTGGTAAATTTTTGAATTTCACAGTATAATGCTGATTTTCTCAAAGTCTCACATTCTAAGAAAGTATAATGAGGCAAAACAAACAACAAACATCTTAAGTTGATTTTTTCCTAGCATCTTTTCCTTCCATCTTTGCTTGTAGAATCTAGACTATTTCATGAACCCAAGATATAATCAGTATCCTTCTTCAGTATGGCCAAAGTGAGTTTCTCATTATTTTACCTCCCCTTCAGGAAATGACTTTTCATCTTGTGTTTTGGGAGCCATAGATGGTTCTGGGCAGGAAACTGGCTTTGGATAGACCCAGCATGTAGATGGCTATTTGGCCTTGCTCCCAGTATAACGATGCAGTTCCCTGTGAAAGGGTATGAGTAGGTTTTGGGGCTCTGGATACCGTGTGGCCTGAAGAGACAAGGGCTCAATGCCAACTCTGCCTGTTTCCAACTGTGTAACCATGTGAGCGTCAAAAATCATGGACGTGCTCTGGTTAACACTGAGTGGGAGCTCAACAAATTATTATTTTTAATTGTTACTTGGACATGGCCAAGTTGACTACACTTTATGTTCTGCTACCTGCCAGTCTGAAAGTGACGCCACAGAAGGTGAACCGCATGTTGGGAGATGCTCCTCATCTGCTTAAATGAGGTGCAAACACAGCCCATGCGCCTGCTCTTCATGACTGTATCTGTACCAGCAATATTTGTATTGGCAAATCACATGCCCCAGTGGGAACTACTTAAGGGGAATTCAATGGATTTCATTCCTTTTATGTAATTGGCCACTTAGTAATAGACGTGTAGGTCTCTTGTGTGGATAAGGATTCTGCCTTTTATGTAAGATATGTGTTGCAATTCAGCTTTCAGGTCCCAGCCCCGGGAAGGCTCCAGGCCTTCACAAACTGGCCCACCCACGAGAAGGAAAGCAATTGTCCAAATGTGGGTAGCTTTTCTTCCCACTGTTGTCAGCTGCTTCCAATTAGCCCCCATATACATAATCCCAGTTTGTGTCTGTATCAGTACAATTCTCCCATGTCAATGTGAATTTTAAGCCACAGAGGGAAAGGGGACAGAGAATATGCTTTCATTCAGCTCTCCTCGTCTCACAC</seq_for_pcr_oligo_design>
          <seq_for_extension_oligo_design>TTCTCATTATTTTACCTCCCCTTCAGGAAATGACTTTTCANCTTGTGTTTTGGGAGCCATAGATGGTTCTGGGCAGGAAAC</seq_for_extension_oligo_design>
        </fp_tdi_platform>
      </input_parameters>
      <output_design>
        <strand>forward</strand>
        <fp_tdi_platform>
          <pcr_primer_forward>ATGATTTTAGATTGG</pcr_primer_forward>
          <pcr_primer_reverse>TTAGTTTAGGTGGGGAA</pcr_primer_reverse>
          <extension_primer>TTAGATGGCCATTACC</extension_primer>
        </fp_tdi_platform>
      </output_design>
    </assay>
    <!--Baylor's Inversion probe platform -->
    <assay lsid="urn:lsid:bcm.hapmap.org:Assay:rs003424-34:1">
      <snp_assayed lsid="urn:lsid:ncbi.nlm.nih.gov:dbSNP/refSNP:rs20965:96"/>
      <protocol_used lsid="urn:LSID:bcm.hapmap.org:Protocol:assay-design_0001:1"/>
      <batch type="multiplex-pool">batch_2003-02-11_ff</batch>
      <status>
        <pass/>
      </status>
      <input_parameters>
        <mip_platform>
          <seq_for_mip_probe_design>atgatgacttatgtgggggcagtggaaagaagagggcagaaccaggaccactgcacaggtagaattgacctcgttattgaatattcagcagcttctcaca[R]tctagagaactattgaaggctctccattcacttcctttatctacttcttggcccacactcattctccatgcaaacattagttctctcctaatcatccagg</seq_for_mip_probe_design>
        </mip_platform>
      </input_parameters>
      <output_design>
        <strand>forward</strand>
        <mip_platform>
          <mip_probe>TCTAGAGAACTATTGAAGGCTACGGCTCAACGTTCCTATTCGGTTUUUTTGCAAATGTTATCGAGGTCCGGCCCCGCACAGAAATGCTTGAATTTAAAATTCAGCAGCTTCTCACA</mip_probe>
        </mip_platform>
      </output_design>
    </assay>
  </assays>
</assay_submission>
