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<EXPERIMENT_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <EXPERIMENT alias="mES control" accession="SRX304982" center_name="uci">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX304982</PRIMARY_ID>
      <SUBMITTER_ID namespace="uci">mES control</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>mRNA alternative polyadenylation in mouse embryonic control stem cells</TITLE>
    <STUDY_REF accession="SRP025988">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP025988</PRIMARY_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>Total RNA isolated from mouse embryonic stem cell line E14Tg2a transfected with control siRNAs</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS444306">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS444306</PRIMARY_ID>
          <SUBMITTER_ID namespace="uci">Control</SUBMITTER_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>mES control</LIBRARY_NAME>
        <LIBRARY_STRATEGY>OTHER</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>TRANSCRIPTOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>other</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <SINGLE/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>0</SPOT_LENGTH>
          <READ_SPEC>
            <READ_INDEX>0</READ_INDEX>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Forward</READ_TYPE>
            <BASE_COORD>1</BASE_COORD>
          </READ_SPEC>
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <HELICOS>
        <INSTRUMENT_MODEL>Helicos HeliScope</INSTRUMENT_MODEL>
      </HELICOS>
    </PLATFORM>
    <PROCESSING/>
  </EXPERIMENT>
  <EXPERIMENT alias="mES-Fip1" accession="SRX304983" center_name="uci">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX304983</PRIMARY_ID>
      <SUBMITTER_ID namespace="uci">mES-Fip1</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>mRNA alternative polyadenylation in mouse embryonic Fip1 RNAi stem cells</TITLE>
    <STUDY_REF accession="SRP025988">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP025988</PRIMARY_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>Total RNA isolated from mouse embryonic stem cell line E14Tg2a transfected with Fip1l1-specific siRNA</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS444307">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS444307</PRIMARY_ID>
          <SUBMITTER_ID namespace="uci">Fip1</SUBMITTER_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>mES Fip1</LIBRARY_NAME>
        <LIBRARY_STRATEGY>OTHER</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>TRANSCRIPTOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>other</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <SINGLE/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>0</SPOT_LENGTH>
          <READ_SPEC>
            <READ_INDEX>0</READ_INDEX>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Forward</READ_TYPE>
            <BASE_COORD>1</BASE_COORD>
          </READ_SPEC>
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <HELICOS>
        <INSTRUMENT_MODEL>Helicos HeliScope</INSTRUMENT_MODEL>
      </HELICOS>
    </PLATFORM>
    <PROCESSING/>
  </EXPERIMENT>
  <EXPERIMENT alias="HeLa-Fip1" accession="SRX388391" center_name="uci">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX388391</PRIMARY_ID>
      <SUBMITTER_ID namespace="uci">HeLa-Fip1</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>mRNA alternative polyadenylation in human Fip1 RNAi HeLa cells</TITLE>
    <STUDY_REF accession="SRP025988">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP025988</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioProject">PRJNA207978</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>HeLa cells were transfected with shRNA construct and/or siRNAs using Lipofectamine 2000 (Invitrogen)</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS512278">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS512278</PRIMARY_ID>
          <EXTERNAL_ID namespace="BioSample">SAMN02437970</EXTERNAL_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>HeLa Fip1</LIBRARY_NAME>
        <LIBRARY_STRATEGY>OTHER</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>TRANSCRIPTOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>other</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <SINGLE/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>0</SPOT_LENGTH>
          <READ_SPEC>
            <READ_INDEX>0</READ_INDEX>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Forward</READ_TYPE>
            <BASE_COORD>1</BASE_COORD>
          </READ_SPEC>
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <HELICOS>
        <INSTRUMENT_MODEL>Helicos HeliScope</INSTRUMENT_MODEL>
      </HELICOS>
    </PLATFORM>
    <PROCESSING/>
  </EXPERIMENT>
  <EXPERIMENT alias="Fip1-iCLIP" center_name="uci" accession="SRX390359">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX390359</PRIMARY_ID>
      <SUBMITTER_ID namespace="uci">Fip1-iCLIP</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>Fip1 iCLIP-seq</TITLE>
    <STUDY_REF accession="SRP025988">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP025988</PRIMARY_ID>
        <EXTERNAL_ID namespace="BioProject">PRJNA207978</EXTERNAL_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>iCLIP-seq libraries were prepared as described by Konig et al, NSMB (2010) 17: 909; the antibody used was purchased from Bethyl Laboratories (Cat#: A301-092A; lot #: A301-092A-1); iCLIP-seq: RNAs were extracted from immunoprecipitated protein-RNA complexes;</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS444306">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS444306</PRIMARY_ID>
          <SUBMITTER_ID namespace="uci">Control</SUBMITTER_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Fip1 iCLIP-seq</LIBRARY_NAME>
        <LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>TRANSCRIPTOMIC</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RT-PCR</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <SINGLE/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>42</SPOT_LENGTH>
          <READ_SPEC>
            <READ_INDEX>0</READ_INDEX>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Forward</READ_TYPE>
            <BASE_COORD>1</BASE_COORD>
          </READ_SPEC>
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 2000</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
    <PROCESSING/>
  </EXPERIMENT>
</EXPERIMENT_SET>
