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      <PRIMARY_ID>SRX4232634</PRIMARY_ID>
      <SUBMITTER_ID namespace="Yale University">Cte-07</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>SMARTT: C. tetani glycine riboswitch (type-1) transcribed with 2.75 mM Gly - Replicate A</TITLE>
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      <IDENTIFIERS>
        <PRIMARY_ID>SRP150789</PRIMARY_ID>
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      <DESIGN_DESCRIPTION>A mutagenized library of template DNA was made by error-prone PCR using the GeneMorph II Random Mutagenesis Kit (Agilent Technologies). Mutations were introduced to the aptamer and expression platform domains using a 16 cycle error-prone PCR reaction. Nonmutagenized regions upstream of the aptamer, including a promoter, were added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific). This library was used as DNA template for an in vitro transcription reaction containing the specified concentration of ligand (glycine or alanine). DNA template was removed by DNase treatment with TURBO DNase (Thermo Fisher Scientific). A pre-adenylated adaptor was then added to the 3' end using T4 RNA Ligase II, Trunc. K227Q (NEB). Using this adaptor as a handle, the RNA was reverse-transcribed into DNA with SuperScript III (Thermo Fisher Scientific). Illumina adaptors were then added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific).</DESIGN_DESCRIPTION>
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          <PRIMARY_ID>SRS3431274</PRIMARY_ID>
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        <LIBRARY_NAME>Cte-07</LIBRARY_NAME>
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          <SPOT_LENGTH>300</SPOT_LENGTH>
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            <READ_INDEX>1</READ_INDEX>
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      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 4000</INSTRUMENT_MODEL>
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    <IDENTIFIERS>
      <PRIMARY_ID>SRX4232635</PRIMARY_ID>
      <SUBMITTER_ID namespace="Yale University">Cte-05</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>SMARTT: C. tetani glycine riboswitch (type-1) transcribed with 550 uM Gly - Replicate A</TITLE>
    <STUDY_REF accession="SRP150789">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP150789</PRIMARY_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>A mutagenized library of template DNA was made by error-prone PCR using the GeneMorph II Random Mutagenesis Kit (Agilent Technologies). Mutations were introduced to the aptamer and expression platform domains using a 16 cycle error-prone PCR reaction. Nonmutagenized regions upstream of the aptamer, including a promoter, were added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific). This library was used as DNA template for an in vitro transcription reaction containing the specified concentration of ligand (glycine or alanine). DNA template was removed by DNase treatment with TURBO DNase (Thermo Fisher Scientific). A pre-adenylated adaptor was then added to the 3' end using T4 RNA Ligase II, Trunc. K227Q (NEB). Using this adaptor as a handle, the RNA was reverse-transcribed into DNA with SuperScript III (Thermo Fisher Scientific). Illumina adaptors were then added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific).</DESIGN_DESCRIPTION>
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          <PRIMARY_ID>SRS3431275</PRIMARY_ID>
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        <LIBRARY_NAME>Cte-05</LIBRARY_NAME>
        <LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>OTHER</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RT-PCR</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED/>
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          <SPOT_LENGTH>300</SPOT_LENGTH>
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            <READ_INDEX>0</READ_INDEX>
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            <READ_INDEX>1</READ_INDEX>
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      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 4000</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
  </EXPERIMENT>
  <EXPERIMENT alias="Cte-08" accession="SRX4232636">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX4232636</PRIMARY_ID>
      <SUBMITTER_ID namespace="Yale University">Cte-08</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>SMARTT: C. tetani glycine riboswitch (type-1) transcribed with 6 mM Gly - Replicate A</TITLE>
    <STUDY_REF accession="SRP150789">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP150789</PRIMARY_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>A mutagenized library of template DNA was made by error-prone PCR using the GeneMorph II Random Mutagenesis Kit (Agilent Technologies). Mutations were introduced to the aptamer and expression platform domains using a 16 cycle error-prone PCR reaction. Nonmutagenized regions upstream of the aptamer, including a promoter, were added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific). This library was used as DNA template for an in vitro transcription reaction containing the specified concentration of ligand (glycine or alanine). DNA template was removed by DNase treatment with TURBO DNase (Thermo Fisher Scientific). A pre-adenylated adaptor was then added to the 3' end using T4 RNA Ligase II, Trunc. K227Q (NEB). Using this adaptor as a handle, the RNA was reverse-transcribed into DNA with SuperScript III (Thermo Fisher Scientific). Illumina adaptors were then added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific).</DESIGN_DESCRIPTION>
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        <IDENTIFIERS>
          <PRIMARY_ID>SRS3431273</PRIMARY_ID>
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      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Cte-08</LIBRARY_NAME>
        <LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>OTHER</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RT-PCR</LIBRARY_SELECTION>
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          <PAIRED/>
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          <SPOT_LENGTH>300</SPOT_LENGTH>
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            <READ_INDEX>0</READ_INDEX>
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            <BASE_COORD>1</BASE_COORD>
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          <READ_SPEC>
            <READ_INDEX>1</READ_INDEX>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Reverse</READ_TYPE>
            <BASE_COORD>151</BASE_COORD>
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    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 4000</INSTRUMENT_MODEL>
      </ILLUMINA>
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  </EXPERIMENT>
  <EXPERIMENT alias="Cte-14" accession="SRX4232637">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX4232637</PRIMARY_ID>
      <SUBMITTER_ID namespace="Yale University">Cte-14</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>SMARTT: C. tetani glycine riboswitch (type-1) transcribed with 100 mM Ala - Replicate A</TITLE>
    <STUDY_REF accession="SRP150789">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP150789</PRIMARY_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>A mutagenized library of template DNA was made by error-prone PCR using the GeneMorph II Random Mutagenesis Kit (Agilent Technologies). Mutations were introduced to the aptamer and expression platform domains using a 16 cycle error-prone PCR reaction. Nonmutagenized regions upstream of the aptamer, including a promoter, were added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific). This library was used as DNA template for an in vitro transcription reaction containing the specified concentration of ligand (glycine or alanine). DNA template was removed by DNase treatment with TURBO DNase (Thermo Fisher Scientific). A pre-adenylated adaptor was then added to the 3' end using T4 RNA Ligase II, Trunc. K227Q (NEB). Using this adaptor as a handle, the RNA was reverse-transcribed into DNA with SuperScript III (Thermo Fisher Scientific). Illumina adaptors were then added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific).</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS3431280">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS3431280</PRIMARY_ID>
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      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Cte-14</LIBRARY_NAME>
        <LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>OTHER</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RT-PCR</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED/>
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      <SPOT_DESCRIPTOR>
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          <SPOT_LENGTH>300</SPOT_LENGTH>
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            <READ_INDEX>1</READ_INDEX>
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      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 4000</INSTRUMENT_MODEL>
      </ILLUMINA>
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  <EXPERIMENT alias="Cte-12" accession="SRX4232638">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX4232638</PRIMARY_ID>
      <SUBMITTER_ID namespace="Yale University">Cte-12</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>SMARTT: C. tetani glycine riboswitch (type-1) transcribed with 100 mM Gly - Replicate A</TITLE>
    <STUDY_REF accession="SRP150789">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP150789</PRIMARY_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>A mutagenized library of template DNA was made by error-prone PCR using the GeneMorph II Random Mutagenesis Kit (Agilent Technologies). Mutations were introduced to the aptamer and expression platform domains using a 16 cycle error-prone PCR reaction. Nonmutagenized regions upstream of the aptamer, including a promoter, were added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific). This library was used as DNA template for an in vitro transcription reaction containing the specified concentration of ligand (glycine or alanine). DNA template was removed by DNase treatment with TURBO DNase (Thermo Fisher Scientific). A pre-adenylated adaptor was then added to the 3' end using T4 RNA Ligase II, Trunc. K227Q (NEB). Using this adaptor as a handle, the RNA was reverse-transcribed into DNA with SuperScript III (Thermo Fisher Scientific). Illumina adaptors were then added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific).</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS3431277">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS3431277</PRIMARY_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Cte-12</LIBRARY_NAME>
        <LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>OTHER</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RT-PCR</LIBRARY_SELECTION>
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          <PAIRED/>
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          <SPOT_LENGTH>300</SPOT_LENGTH>
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            <READ_INDEX>0</READ_INDEX>
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          <READ_SPEC>
            <READ_INDEX>1</READ_INDEX>
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    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 4000</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
  </EXPERIMENT>
  <EXPERIMENT alias="Cte-11" accession="SRX4232639">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX4232639</PRIMARY_ID>
      <SUBMITTER_ID namespace="Yale University">Cte-11</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>SMARTT: C. tetani glycine riboswitch (type-1) transcribed with 50 mM Gly - Replicate A</TITLE>
    <STUDY_REF accession="SRP150789">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP150789</PRIMARY_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>A mutagenized library of template DNA was made by error-prone PCR using the GeneMorph II Random Mutagenesis Kit (Agilent Technologies). Mutations were introduced to the aptamer and expression platform domains using a 16 cycle error-prone PCR reaction. Nonmutagenized regions upstream of the aptamer, including a promoter, were added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific). This library was used as DNA template for an in vitro transcription reaction containing the specified concentration of ligand (glycine or alanine). DNA template was removed by DNase treatment with TURBO DNase (Thermo Fisher Scientific). A pre-adenylated adaptor was then added to the 3' end using T4 RNA Ligase II, Trunc. K227Q (NEB). Using this adaptor as a handle, the RNA was reverse-transcribed into DNA with SuperScript III (Thermo Fisher Scientific). Illumina adaptors were then added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific).</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS3431282">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS3431282</PRIMARY_ID>
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        <LIBRARY_NAME>Cte-11</LIBRARY_NAME>
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          <PAIRED/>
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          <SPOT_LENGTH>300</SPOT_LENGTH>
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          <READ_SPEC>
            <READ_INDEX>1</READ_INDEX>
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      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 4000</INSTRUMENT_MODEL>
      </ILLUMINA>
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  </EXPERIMENT>
  <EXPERIMENT alias="Cte-04" accession="SRX4232640">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX4232640</PRIMARY_ID>
      <SUBMITTER_ID namespace="Yale University">Cte-04</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>SMARTT: C. tetani glycine riboswitch (type-1) transcribed with 225 uM Gly - Replicate A</TITLE>
    <STUDY_REF accession="SRP150789">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP150789</PRIMARY_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>A mutagenized library of template DNA was made by error-prone PCR using the GeneMorph II Random Mutagenesis Kit (Agilent Technologies). Mutations were introduced to the aptamer and expression platform domains using a 16 cycle error-prone PCR reaction. Nonmutagenized regions upstream of the aptamer, including a promoter, were added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific). This library was used as DNA template for an in vitro transcription reaction containing the specified concentration of ligand (glycine or alanine). DNA template was removed by DNase treatment with TURBO DNase (Thermo Fisher Scientific). A pre-adenylated adaptor was then added to the 3' end using T4 RNA Ligase II, Trunc. K227Q (NEB). Using this adaptor as a handle, the RNA was reverse-transcribed into DNA with SuperScript III (Thermo Fisher Scientific). Illumina adaptors were then added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific).</DESIGN_DESCRIPTION>
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          <PRIMARY_ID>SRS3431278</PRIMARY_ID>
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        <LIBRARY_NAME>Cte-04</LIBRARY_NAME>
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          <PAIRED/>
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          <SPOT_LENGTH>300</SPOT_LENGTH>
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          <READ_SPEC>
            <READ_INDEX>1</READ_INDEX>
            <READ_CLASS>Application Read</READ_CLASS>
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    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 4000</INSTRUMENT_MODEL>
      </ILLUMINA>
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    <IDENTIFIERS>
      <PRIMARY_ID>SRX4232641</PRIMARY_ID>
      <SUBMITTER_ID namespace="Yale University">Cte-03</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>SMARTT: C. tetani glycine riboswitch (type-1) transcribed with 90 uM Gly - Replicate A</TITLE>
    <STUDY_REF accession="SRP150789">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP150789</PRIMARY_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>A mutagenized library of template DNA was made by error-prone PCR using the GeneMorph II Random Mutagenesis Kit (Agilent Technologies). Mutations were introduced to the aptamer and expression platform domains using a 16 cycle error-prone PCR reaction. Nonmutagenized regions upstream of the aptamer, including a promoter, were added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific). This library was used as DNA template for an in vitro transcription reaction containing the specified concentration of ligand (glycine or alanine). DNA template was removed by DNase treatment with TURBO DNase (Thermo Fisher Scientific). A pre-adenylated adaptor was then added to the 3' end using T4 RNA Ligase II, Trunc. K227Q (NEB). Using this adaptor as a handle, the RNA was reverse-transcribed into DNA with SuperScript III (Thermo Fisher Scientific). Illumina adaptors were then added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific).</DESIGN_DESCRIPTION>
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          <PRIMARY_ID>SRS3431276</PRIMARY_ID>
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      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Cte-03</LIBRARY_NAME>
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        <LIBRARY_SELECTION>RT-PCR</LIBRARY_SELECTION>
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          <PAIRED/>
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          <SPOT_LENGTH>300</SPOT_LENGTH>
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          <READ_SPEC>
            <READ_INDEX>1</READ_INDEX>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Reverse</READ_TYPE>
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    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 4000</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
  </EXPERIMENT>
  <EXPERIMENT alias="Cte-02" accession="SRX4232642">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX4232642</PRIMARY_ID>
      <SUBMITTER_ID namespace="Yale University">Cte-02</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>SMARTT: C. tetani glycine riboswitch (type-1) transcribed with 30 uM Gly - Replicate A</TITLE>
    <STUDY_REF accession="SRP150789">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP150789</PRIMARY_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>A mutagenized library of template DNA was made by error-prone PCR using the GeneMorph II Random Mutagenesis Kit (Agilent Technologies). Mutations were introduced to the aptamer and expression platform domains using a 16 cycle error-prone PCR reaction. Nonmutagenized regions upstream of the aptamer, including a promoter, were added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific). This library was used as DNA template for an in vitro transcription reaction containing the specified concentration of ligand (glycine or alanine). DNA template was removed by DNase treatment with TURBO DNase (Thermo Fisher Scientific). A pre-adenylated adaptor was then added to the 3' end using T4 RNA Ligase II, Trunc. K227Q (NEB). Using this adaptor as a handle, the RNA was reverse-transcribed into DNA with SuperScript III (Thermo Fisher Scientific). Illumina adaptors were then added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific).</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS3431279">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS3431279</PRIMARY_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Cte-02</LIBRARY_NAME>
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        <LIBRARY_SELECTION>RT-PCR</LIBRARY_SELECTION>
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          <PAIRED/>
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          <SPOT_LENGTH>300</SPOT_LENGTH>
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            <READ_TYPE>Forward</READ_TYPE>
            <BASE_COORD>1</BASE_COORD>
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          <READ_SPEC>
            <READ_INDEX>1</READ_INDEX>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Reverse</READ_TYPE>
            <BASE_COORD>151</BASE_COORD>
          </READ_SPEC>
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 4000</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
  </EXPERIMENT>
  <EXPERIMENT alias="Cte-01" accession="SRX4232643">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX4232643</PRIMARY_ID>
      <SUBMITTER_ID namespace="Yale University">Cte-01</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>SMARTT: C. tetani glycine riboswitch (type-1) transcribed with 0 uM Gly - Replicate A</TITLE>
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      <IDENTIFIERS>
        <PRIMARY_ID>SRP150789</PRIMARY_ID>
      </IDENTIFIERS>
    </STUDY_REF>
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      <DESIGN_DESCRIPTION>A mutagenized library of template DNA was made by error-prone PCR using the GeneMorph II Random Mutagenesis Kit (Agilent Technologies). Mutations were introduced to the aptamer and expression platform domains using a 16 cycle error-prone PCR reaction. Nonmutagenized regions upstream of the aptamer, including a promoter, were added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific). This library was used as DNA template for an in vitro transcription reaction containing the specified concentration of ligand (glycine or alanine). DNA template was removed by DNase treatment with TURBO DNase (Thermo Fisher Scientific). A pre-adenylated adaptor was then added to the 3' end using T4 RNA Ligase II, Trunc. K227Q (NEB). Using this adaptor as a handle, the RNA was reverse-transcribed into DNA with SuperScript III (Thermo Fisher Scientific). Illumina adaptors were then added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific).</DESIGN_DESCRIPTION>
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        <IDENTIFIERS>
          <PRIMARY_ID>SRS3431281</PRIMARY_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
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        <LIBRARY_NAME>Cte-01</LIBRARY_NAME>
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        <LIBRARY_SOURCE>OTHER</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RT-PCR</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED/>
        </LIBRARY_LAYOUT>
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          <SPOT_LENGTH>300</SPOT_LENGTH>
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            <READ_INDEX>0</READ_INDEX>
            <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_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Reverse</READ_TYPE>
            <BASE_COORD>151</BASE_COORD>
          </READ_SPEC>
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
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      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 4000</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
  </EXPERIMENT>
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    <IDENTIFIERS>
      <PRIMARY_ID>SRX4232644</PRIMARY_ID>
      <SUBMITTER_ID namespace="Yale University">Cte-06</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>SMARTT: C. tetani glycine riboswitch (type-1) transcribed with 1.25 mM Gly - Replicate A</TITLE>
    <STUDY_REF accession="SRP150789">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP150789</PRIMARY_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>A mutagenized library of template DNA was made by error-prone PCR using the GeneMorph II Random Mutagenesis Kit (Agilent Technologies). Mutations were introduced to the aptamer and expression platform domains using a 16 cycle error-prone PCR reaction. Nonmutagenized regions upstream of the aptamer, including a promoter, were added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific). This library was used as DNA template for an in vitro transcription reaction containing the specified concentration of ligand (glycine or alanine). DNA template was removed by DNase treatment with TURBO DNase (Thermo Fisher Scientific). A pre-adenylated adaptor was then added to the 3' end using T4 RNA Ligase II, Trunc. K227Q (NEB). Using this adaptor as a handle, the RNA was reverse-transcribed into DNA with SuperScript III (Thermo Fisher Scientific). Illumina adaptors were then added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific).</DESIGN_DESCRIPTION>
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        <IDENTIFIERS>
          <PRIMARY_ID>SRS3431283</PRIMARY_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Cte-06</LIBRARY_NAME>
        <LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>OTHER</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RT-PCR</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>300</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>
          <READ_SPEC>
            <READ_INDEX>1</READ_INDEX>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Reverse</READ_TYPE>
            <BASE_COORD>151</BASE_COORD>
          </READ_SPEC>
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 4000</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
  </EXPERIMENT>
  <EXPERIMENT alias="Cte-10" accession="SRX4232645">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX4232645</PRIMARY_ID>
      <SUBMITTER_ID namespace="Yale University">Cte-10</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>SMARTT: C. tetani glycine riboswitch (type-1) transcribed with 25 mM Gly - Replicate A</TITLE>
    <STUDY_REF accession="SRP150789">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP150789</PRIMARY_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>A mutagenized library of template DNA was made by error-prone PCR using the GeneMorph II Random Mutagenesis Kit (Agilent Technologies). Mutations were introduced to the aptamer and expression platform domains using a 16 cycle error-prone PCR reaction. Nonmutagenized regions upstream of the aptamer, including a promoter, were added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific). This library was used as DNA template for an in vitro transcription reaction containing the specified concentration of ligand (glycine or alanine). DNA template was removed by DNase treatment with TURBO DNase (Thermo Fisher Scientific). A pre-adenylated adaptor was then added to the 3' end using T4 RNA Ligase II, Trunc. K227Q (NEB). Using this adaptor as a handle, the RNA was reverse-transcribed into DNA with SuperScript III (Thermo Fisher Scientific). Illumina adaptors were then added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific).</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS3431284">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS3431284</PRIMARY_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Cte-10</LIBRARY_NAME>
        <LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>OTHER</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RT-PCR</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>300</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>
          <READ_SPEC>
            <READ_INDEX>1</READ_INDEX>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Reverse</READ_TYPE>
            <BASE_COORD>151</BASE_COORD>
          </READ_SPEC>
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 4000</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
  </EXPERIMENT>
  <EXPERIMENT alias="Cte-09" accession="SRX4232646">
    <IDENTIFIERS>
      <PRIMARY_ID>SRX4232646</PRIMARY_ID>
      <SUBMITTER_ID namespace="Yale University">Cte-09</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>SMARTT: C. tetani glycine riboswitch (type-1) transcribed with 12.5 mM Gly - Replicate A</TITLE>
    <STUDY_REF accession="SRP150789">
      <IDENTIFIERS>
        <PRIMARY_ID>SRP150789</PRIMARY_ID>
      </IDENTIFIERS>
    </STUDY_REF>
    <DESIGN>
      <DESIGN_DESCRIPTION>A mutagenized library of template DNA was made by error-prone PCR using the GeneMorph II Random Mutagenesis Kit (Agilent Technologies). Mutations were introduced to the aptamer and expression platform domains using a 16 cycle error-prone PCR reaction. Nonmutagenized regions upstream of the aptamer, including a promoter, were added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific). This library was used as DNA template for an in vitro transcription reaction containing the specified concentration of ligand (glycine or alanine). DNA template was removed by DNase treatment with TURBO DNase (Thermo Fisher Scientific). A pre-adenylated adaptor was then added to the 3' end using T4 RNA Ligase II, Trunc. K227Q (NEB). Using this adaptor as a handle, the RNA was reverse-transcribed into DNA with SuperScript III (Thermo Fisher Scientific). Illumina adaptors were then added through a two-step PCR reaction with Phusion HF polymerase (NEB or Thermo Fisher Scientific).</DESIGN_DESCRIPTION>
      <SAMPLE_DESCRIPTOR accession="SRS3431287">
        <IDENTIFIERS>
          <PRIMARY_ID>SRS3431287</PRIMARY_ID>
        </IDENTIFIERS>
      </SAMPLE_DESCRIPTOR>
      <LIBRARY_DESCRIPTOR>
        <LIBRARY_NAME>Cte-09</LIBRARY_NAME>
        <LIBRARY_STRATEGY>RNA-Seq</LIBRARY_STRATEGY>
        <LIBRARY_SOURCE>OTHER</LIBRARY_SOURCE>
        <LIBRARY_SELECTION>RT-PCR</LIBRARY_SELECTION>
        <LIBRARY_LAYOUT>
          <PAIRED/>
        </LIBRARY_LAYOUT>
      </LIBRARY_DESCRIPTOR>
      <SPOT_DESCRIPTOR>
        <SPOT_DECODE_SPEC>
          <SPOT_LENGTH>300</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>
          <READ_SPEC>
            <READ_INDEX>1</READ_INDEX>
            <READ_CLASS>Application Read</READ_CLASS>
            <READ_TYPE>Reverse</READ_TYPE>
            <BASE_COORD>151</BASE_COORD>
          </READ_SPEC>
        </SPOT_DECODE_SPEC>
      </SPOT_DESCRIPTOR>
    </DESIGN>
    <PLATFORM>
      <ILLUMINA>
        <INSTRUMENT_MODEL>Illumina HiSeq 4000</INSTRUMENT_MODEL>
      </ILLUMINA>
    </PLATFORM>
  </EXPERIMENT>
</EXPERIMENT_SET>
