Difference between revisions of "Team:TUDelft/Primers/Main"

 
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Line 1: Line 1:
 
<html>       
 
<html>       
 +
<head>
 +
<style>
 +
table td + td + td + td {
 +
  font-family: Courier New;
 +
  text-transform: uppercase;
 +
  word-break:break-all;
 +
}
 +
</style>
 +
</head>
 +
  
 
<body>
 
<body>
Line 17: Line 27:
  
 
<div class="col-lg-10 col-md-10 col-sm-10 col-xs-10 nowbg">  
 
<div class="col-lg-10 col-md-10 col-sm-10 col-xs-10 nowbg">  
−
            <p>stuff to write here</p>
 
  
 
       <div class="spcmkr" id="primers"></div>
 
       <div class="spcmkr" id="primers"></div>
Line 59: Line 68:
 
     <td>fw_Tn5_afterC</td>
 
     <td>fw_Tn5_afterC</td>
 
     <td>Fusion Protein</td>
 
     <td>Fusion Protein</td>
−
     <td style="word-break:break-all;">tataGGCCGGCCtAAACTGGGCGGCGGCGCGCCGGCGGTGGGCGGCGGCCCGAAAGCGGCGGATAAAatgattaccagtgcactgcatc</td>
+
     <td>tataGGCCGGCCtAAACTGGGCGGCGGCGCGCCGGCGGTGGGCGGCGGCCCGAAAGCGGCGGATAAAatgattaccagtgcactgcatc</td>
 
   </tr>
 
   </tr>
 
   <tr class="tableevengrnbl">
 
   <tr class="tableevengrnbl">
Line 419: Line 428:
 
     <td>fw_1_AUpart</td>
 
     <td>fw_1_AUpart</td>
 
     <td>d-AuNPs</td>
 
     <td>d-AuNPs</td>
−
     <td><Cy-GATCGAATTCGCGGCCGCTTC/td>
+
     <td>Cy-GATCGAATTCGCGGCCGCTTC</td>
 
   </tr>
 
   </tr>
 
   <tr class="tableevengrnbl">
 
   <tr class="tableevengrnbl">
Line 621: Line 630:
 
<tr class="tableunevengrnbl">
 
<tr class="tableunevengrnbl">
 
     <td>099</td>
 
     <td>099</td>
−
     <td></td>
+
     <td>fw_BB_sgRNA_EPO1</td>
−
     <td></td>
+
     <td>BioBrick</td>
−
     <td></td>
+
     <td>gaattcgcggccgcttctagagGGAGGCCGAGAATATCAC</td>
 
   </tr>
 
   </tr>
 
<tr class="tableevengrnbl">
 
<tr class="tableevengrnbl">
 
     <td>100</td>
 
     <td>100</td>
−
     <td></td>
+
     <td>fw_BB_sgRNA_EPO2</td>
−
     <td></td>
+
     <td>BioBrick</td>
−
     <td></td>
+
     <td>gaattcgcggccgcttctagagACAGCCCGTCGTGATATTCT</td>
 
   </tr>
 
   </tr>
−
  <tr class="tableunevengrnbl">
+
<tr class="tableunevengrnbl">
 
     <td>101</td>
 
     <td>101</td>
 +
    <td>fw_BB_T7_sgRNA</td>
 +
    <td>BioBrick</td>
 +
    <td>gaattcgcggccgcttctagagaagcTAATACGACTCACTATAGG</td>
 +
  </tr>
 +
<tr class="tableevengrnbl">
 +
    <td>102</td>
 +
    <td>rv_BB_sgRNA</td>
 +
    <td>BioBrick</td>
 +
    <td>ctgcagcggccgctactagtaGCACCGACTCGGTGCCAC</td>
 +
  </tr>
 +
<tr class="tableevengrnbl">
 +
    <td>103</td>
 +
    <td>SeqTim_01</td>
 +
    <td>Sequencing</td>
 +
    <td>GATATGAATAAATTGCAGTTTGTCGGGCAGCAGGCCGTAGA</td>
 +
  </tr>
 +
  <tr class="tableunevengrnbl">
 +
    <td>104</td>
 +
    <td>SeqTim_02</td>
 +
    <td>Sequencing</td>
 +
    <td>CATCATTGGCAACGCTACCCTCCATCCTCTTCCAGGCAT</td>
 +
  </tr>
 +
  <tr class="tableevengrnbl">
 +
    <td>105</td>
 +
    <td>SeqTim_03</td>
 +
    <td>Sequencing</td>
 +
    <td>TCTACGGCCTGCTGCCCGACAAACTGCAATTTATTCATATC</td>
 +
  </tr>
 +
  <tr class="tableunevengrnbl">
 +
    <td>106</td>
 +
    <td>SeqTim_04</td>
 +
    <td>Sequencing</td>
 +
    <td>ATGCCTGGAAGAGGATGGAGGGTAGCGTTGCCAATGATG</td>
 +
  </tr>
 +
  <tr class="tableevengrnbl">
 +
    <td>107</td>
 +
    <td>SeqTim_05</td>
 +
    <td>Sequencing</td>
 +
    <td>TTCGGGCTCTGGGAGCCCAGccgcctccatccagtctatt</td>
 +
  </tr>
 +
  <tr class="tableunevengrnbl">
 +
    <td>108</td>
 +
    <td>SeqTim_06</td>
 +
    <td>Sequencing</td>
 +
    <td>GGAGGGGAGATGGCTTCCTTgaatgaagccataccaaacg</td>
 +
  </tr>
 +
  <tr class="tableevengrnbl">
 +
    <td>109</td>
 +
    <td>SeqTim_07</td>
 +
    <td>Sequencing</td>
 +
    <td>cgtttggtatggcttcattcAAGGAAGCCATCTCCCCTCC</td>
 +
  </tr>
 +
  <tr class="tableunevengrnbl">
 +
    <td>110</td>
 +
    <td>SeqTim_08</td>
 +
    <td>Sequencing</td>
 +
    <td>aatagactggatggaggcggCTGGGCTCCCAGAGCCCGAA</td>
 +
  </tr>
 +
  <tr class="tableunevengrnbl">
 +
    <td>111</td>
 +
    <td>SeqTim_10</td>
 +
    <td>Sequencing</td>
 +
    <td>P-CTGTCTCTTATACACATCTATGCGCTTCGAA</td>
 +
  </tr>
 +
  <tr class="tableunevengrnbl">
 +
    <td>112</td>
 +
    <td>SeqTim_11</td>
 +
    <td>Sequencing</td>
 +
    <td>AGCTTCGCGTATCTACACATATTCTCTGTC</td>
 +
  </tr>
 +
  <tr class="tableunevengrnbl">
 +
    <td>113</td>
 +
    <td>SeqTim_12</td>
 +
    <td>Sequencing</td>
 +
    <td>P-AGCTTCGCGTATCTACACATATTCTCTGTC</td>
 +
  </tr>
 +
 +
 +
 +
 +
  <tr class="tableunevengrnbl">
 +
    <td>IV001</td>
 
     <td>fw_IV1</td>
 
     <td>fw_IV1</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 638: Line 729:
 
   </tr>
 
   </tr>
 
   <tr class="tableevengrnbl">
 
   <tr class="tableevengrnbl">
−
     <td>102</td>
+
     <td>IV002</td>
 
     <td>rv_IV1</td>
 
     <td>rv_IV1</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 644: Line 735:
 
   </tr>
 
   </tr>
 
   <tr class="tableunevengrnbl">
 
   <tr class="tableunevengrnbl">
−
     <td>103</td>
+
     <td>IV003</td>
 
     <td>fw_IV2</td>
 
     <td>fw_IV2</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 650: Line 741:
 
   </tr>
 
   </tr>
 
   <tr class="tableevengrnbl">
 
   <tr class="tableevengrnbl">
−
     <td>104</td>
+
     <td>IV004</td>
 
     <td>rv_IV2</td>
 
     <td>rv_IV2</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 656: Line 747:
 
   </tr>
 
   </tr>
 
   <tr class="tableunevengrnbl">
 
   <tr class="tableunevengrnbl">
−
     <td>105</td>
+
     <td>IV005</td>
 
     <td>fw_KanR</td>
 
     <td>fw_KanR</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 662: Line 753:
 
   </tr>
 
   </tr>
 
   <tr class="tableevengrnbl">
 
   <tr class="tableevengrnbl">
−
     <td>106</td>
+
     <td>IV006</td>
 
     <td>rv_KanR</td>
 
     <td>rv_KanR</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 668: Line 759:
 
   </tr>
 
   </tr>
 
   <tr class="tableunevengrnbl">
 
   <tr class="tableunevengrnbl">
−
     <td>107</td>
+
     <td>IV007</td>
 
     <td>fw_diagnostic</td>
 
     <td>fw_diagnostic</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 674: Line 765:
 
   </tr>
 
   </tr>
 
   <tr class="tableevengrnbl">
 
   <tr class="tableevengrnbl">
−
     <td>108</td>
+
     <td>IV008</td>
 
     <td>rv_diagnostic</td>
 
     <td>rv_diagnostic</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 680: Line 771:
 
   </tr>
 
   </tr>
 
   <tr class="tableunevengrnbl">
 
   <tr class="tableunevengrnbl">
−
     <td>109</td>
+
     <td>IV009</td>
 
     <td>fw_KanRCassetteME</td>
 
     <td>fw_KanRCassetteME</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 686: Line 777:
 
   </tr>
 
   </tr>
 
   <tr class="tableevengrnbl">
 
   <tr class="tableevengrnbl">
−
     <td>110</td>
+
     <td>IV010</td>
 
     <td>rv_KanRCassetteME</td>
 
     <td>rv_KanRCassetteME</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 692: Line 783:
 
   </tr>
 
   </tr>
 
   <tr class="tableunevengrnbl">
 
   <tr class="tableunevengrnbl">
−
     <td>111</td>
+
     <td>IV011</td>
 
     <td>fw_KanRCassette</td>
 
     <td>fw_KanRCassette</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 698: Line 789:
 
   </tr>
 
   </tr>
 
   <tr class="tableevengrnbl">
 
   <tr class="tableevengrnbl">
−
     <td>112</td>
+
     <td>IV012</td>
 
     <td>rv_KanRCassette</td>
 
     <td>rv_KanRCassette</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 704: Line 795:
 
   </tr>
 
   </tr>
 
   <tr class="tableunevengrnbl">
 
   <tr class="tableunevengrnbl">
−
     <td>113</td>
+
     <td>IV013</td>
 
     <td>fw_KanRCassetteME</td>
 
     <td>fw_KanRCassetteME</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 710: Line 801:
 
   </tr>
 
   </tr>
 
   <tr class="tableevengrnbl">
 
   <tr class="tableevengrnbl">
−
     <td>114</td>
+
     <td>IV014</td>
 
     <td>rv_KanRCassetteME</td>
 
     <td>rv_KanRCassetteME</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 716: Line 807:
 
   </tr>
 
   </tr>
 
   <tr class="tableunevengrnbl">
 
   <tr class="tableunevengrnbl">
−
     <td>115</td>
+
     <td>IV015</td>
 
     <td>fw_KanRCassette</td>
 
     <td>fw_KanRCassette</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 722: Line 813:
 
   </tr>
 
   </tr>
 
   <tr class="tableevengrnbl">
 
   <tr class="tableevengrnbl">
−
     <td>116</td>
+
     <td>IV016</td>
 
     <td>rv_KanRCassette</td>
 
     <td>rv_KanRCassette</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 728: Line 819:
 
   </tr>
 
   </tr>
 
   <tr class="tableunevengrnbl">
 
   <tr class="tableunevengrnbl">
−
     <td>117</td>
+
     <td>IV017</td>
 
     <td>fw_KanRMEBiobrick</td>
 
     <td>fw_KanRMEBiobrick</td>
 
     <td>BioBrick</td>
 
     <td>BioBrick</td>
Line 734: Line 825:
 
   </tr>
 
   </tr>
 
   <tr class="tableevengrnbl">
 
   <tr class="tableevengrnbl">
−
     <td>118</td>
+
     <td>IV018</td>
 
     <td>rv_KanRMEBiobrick</td>
 
     <td>rv_KanRMEBiobrick</td>
 
     <td>BioBrick</td>
 
     <td>BioBrick</td>
Line 740: Line 831:
 
   </tr>
 
   </tr>
 
   <tr class="tableunevengrnbl">
 
   <tr class="tableunevengrnbl">
−
     <td>119</td>
+
     <td>IV019</td>
 
     <td>rv_KanR internal</td>
 
     <td>rv_KanR internal</td>
 
     <td>BioBrick</td>
 
     <td>BioBrick</td>
Line 746: Line 837:
 
   </tr>
 
   </tr>
 
   <tr class="tableevengrnbl">
 
   <tr class="tableevengrnbl">
−
     <td>120</td>
+
     <td>IV020</td>
 
     <td>fw_KanR internal</td>
 
     <td>fw_KanR internal</td>
 
     <td>BioBrick</td>
 
     <td>BioBrick</td>
Line 752: Line 843:
 
   </tr>
 
   </tr>
 
   <tr class="tableunevengrnbl">
 
   <tr class="tableunevengrnbl">
−
     <td>121</td>
+
     <td>IV021</td>
 
     <td>fw target seq LacZ</td>
 
     <td>fw target seq LacZ</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 758: Line 849:
 
   </tr>
 
   </tr>
 
   <tr class="tableevengrnbl">
 
   <tr class="tableevengrnbl">
−
     <td>122</td>
+
     <td>IV022</td>
 
     <td>rv target seq LacZ</td>
 
     <td>rv target seq LacZ</td>
 
     <td></em>In Vivo</em></td>
 
     <td></em>In Vivo</em></td>
Line 764: Line 855:
 
   </tr>
 
   </tr>
 
   <tr class="tableunevengrnbl">
 
   <tr class="tableunevengrnbl">
−
     <td>123</td>
+
     <td>IV023</td>
 
     <td>fw_pSB1C3ori</td>
 
     <td>fw_pSB1C3ori</td>
 
     <td>BioBrick</td>
 
     <td>BioBrick</td>
 
     <td>GCAAGCAGCAGATTACGCG</td>
 
     <td>GCAAGCAGCAGATTACGCG</td>
 
   </tr>
 
   </tr>
−
<tr class="tableevengrnbl">
+
</table>
−
     <td>124</td>
+
 
−
     <td>SeqTim_01</td>
+
      <div class="spcmkr" id="ssDNAp"></div>
−
     <td>Sequencing</td>
+
      <h1 class="grnbl">ssDNAp</h1>
−
     <td>GATATGAATAAATTGCAGTTTGTCGGGCAGCAGGCCGTAGA</td>
+
<table>
 +
  <tr class="tableheadergrnbl">
 +
     <th class="tableheadergrnbl">ID</th>
 +
     <th class="tableheadergrnbl">Name</th>
 +
     <th class="tableheadergrnbl">Module</th>
 +
     <th class="tableheadergrnbl">Sequence (5' to 3')</th>
 +
  </tr>
 
   </tr>
 
   </tr>
 
   <tr class="tableunevengrnbl">
 
   <tr class="tableunevengrnbl">
−
     <td>125</td>
+
     <td>001</td>
−
     <td>SeqTim_02</td>
+
     <td>ssDNAp EPO 1</td>
−
     <td>Sequencing</td>
+
     <td>dAuNPs</td>
−
     <td>CATCATTGGCAACGCTACCCTCCATCCTCTTCCAGGCAT</td>
+
     <td>GGAGGCCGAGAATATCACGA</td>
 
   </tr>
 
   </tr>
 
   <tr class="tableevengrnbl">
 
   <tr class="tableevengrnbl">
−
     <td>126</td>
+
     <td>002</td>
−
     <td>SeqTim_03</td>
+
     <td>ssDNAp EPO 2</td>
−
     <td>Sequencing</td>
+
     <td>dAuNPs</td>
−
     <td>TCTACGGCCTGCTGCCCGACAAACTGCAATTTATTCATATC</td>
+
     <td>TCCTGTCCCTGCTGTCGCTC</td>
 
   </tr>
 
   </tr>
 
   <tr class="tableunevengrnbl">
 
   <tr class="tableunevengrnbl">
−
     <td>127</td>
+
     <td>003</td>
−
     <td>SeqTim_04</td>
+
     <td>ssDNAp EPO 3</td>
−
     <td>Sequencing</td>
+
     <td>dAuNPs</td>
−
     <td>ATGCCTGGAAGAGGATGGAGGGTAGCGTTGCCAATGATG</td>
+
     <td>GCCTGGAAGAGGATGGAGGT</td>
 
   </tr>
 
   </tr>
 
   <tr class="tableevengrnbl">
 
   <tr class="tableevengrnbl">
−
     <td>128</td>
+
     <td>004</td>
−
     <td>SeqTim_05</td>
+
     <td>ssDNAp EPO 4</td>
−
     <td>Sequencing</td>
+
     <td>dAuNPs</td>
−
     <td>TTCGGGCTCTGGGAGCCCAGccgcctccatccagtctatt</td>
+
     <td>CTGCATGTGGATAAAGCCGT</td>
 
   </tr>
 
   </tr>
 
   <tr class="tableunevengrnbl">
 
   <tr class="tableunevengrnbl">
−
     <td>129</td>
+
     <td>005</td>
−
     <td>SeqTim_06</td>
+
     <td>ssDNAp EPO 5</td>
−
     <td>Sequencing</td>
+
     <td>dAuNPs</td>
−
     <td>GGAGGGGAGATGGCTTCCTTgaatgaagccataccaaacg</td>
+
     <td>CGAACAATCACTGCTGACAC</td>
 +
  </tr>
 +
</table>
 +
 
 +
 
 +
 
 +
      <div class="spcmkr" id="sgRNA"></div>
 +
      <h1 class="grnbl">sgRNA</h1>
 +
<table>
 +
  <tr class="tableheadergrnbl">
 +
    <th class="tableheadergrnbl">ID</th>
 +
    <th class="tableheadergrnbl">Name</th>
 +
    <th class="tableheadergrnbl">Module</th>
 +
    <th class="tableheadergrnbl">Sequence (5' to 3')</th>
 +
  </tr>
 +
  </tr>
 +
  <tr class="tableunevengrnbl">
 +
    <td>001</td>
 +
    <td>sgRNA EPO 1</td>
 +
    <td>Fusion Protein</td>
 +
<td>aagcTAATACGACTCACTATAGGGGAGGCCGAGAATATCACGAGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTT</td>
 
   </tr>
 
   </tr>
 
   <tr class="tableevengrnbl">
 
   <tr class="tableevengrnbl">
−
     <td>130</td>
+
     <td>002</td>
−
     <td>SeqTim_07</td>
+
     <td>sgRNA EPO 2</td>
−
     <td>Sequencing</td>
+
     <td>Fusion Protein</td>
−
     <td>cgtttggtatggcttcattcAAGGAAGCCATCTCCCCTCC</td>
+
     <td>TAATACGACTCACTATAGGACAGCCCGTCGTGATATTCTGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGC</td>
 +
  </tr>
 +
<tr class="tableunevengrnbl">
 +
    <td>EPO_J1.1</td>
 +
    <td>Targeting EPO exon-exon junction 1, version 1</td>
 +
    <td>Fusion Protein</td>
 +
    <td>GGGTGCACGAATGTCCTGCC</td>
 +
</tr>
 +
<tr class="tableevengrnbl">
 +
    <td>EPO_J1.2 </td>
 +
    <td>Targeting EPO exon-exon junction 1, version 2</td>
 +
    <td>Fusion Protein</td>
 +
    <td>ACGAATGTCCTGCCTGGCTG</td>
 +
</tr>
 +
<tr class="tableunevengrnbl">
 +
    <td>EPO_J2.1</td>
 +
    <td>Targeting EPO exon-exon junction 2, version 1</td>
 +
    <td>Fusion Protein</td>
 +
    <td>GGAGGCCGAGAATATCACGA</td>
 +
</tr>
 +
<tr class="tableevengrnbl">
 +
    <td>EPO_J.2.2</td>
 +
    <td>Targeting EPO exon-exon junction 2, version 2</td>
 +
    <td>Fusion Protein</td>
 +
    <td>ACAGCCCGTCGTGATATTCT</td>
 +
</tr>
 +
<tr class="tableunevengrnbl">
 +
    <td>EPO_J2.3</td>
 +
    <td>Targeting EPO exon-exon junction 2, version 3</td>
 +
    <td>Fusion Protein</td>
 +
    <td>GAGGCCGAGAATATCACGAC</td>
 +
</tr>
 +
<tr class="tableevengrnbl">
 +
    <td>EPO_J3.1</td>
 +
    <td>Targeting EPO exon-exon junction 2, version 2</td>
 +
    <td>Fusion Protein</td>
 +
    <td> CCTGGAAGAGGATGGAGGTC </td>
 +
</tr>
 +
<tr class="tableunevengrnbl">
 +
    <td>EPO_J3.2</td>
 +
    <td>Targeting EPO exon-exon junction 3, version 1</td>
 +
    <td>Fusion Protein</td>
 +
    <td>GAGGATGGAGGTCGGGCAGC</td>
 +
</tr>
 +
<tr class="tableevengrnbl">
 +
    <td>EPO_J3.1</td>
 +
    <td>Targeting EPO exon-exon junction 3, version 2</td>
 +
    <td>Fusion Protein</td>
 +
    <td> CCTGGAAGAGGATGGAGGTC </td>
 +
</tr>
 +
<tr class="tableunevengrnbl">
 +
    <td>EPO_J4.1</td>
 +
    <td>Targeting EPO exon-exon junction 4, version 1</td>
 +
    <td>Fusion Protein</td>
 +
    <td>AGGGGAGATGGCTTCCTTCT </td>
 +
</tr>
 +
<tr class="tableevengrnbl">
 +
    <td>EPO_J4.2</td>
 +
    <td>Targeting EPO exon-exon junction 4, version 2</td>
 +
    <td>Fusion Protein</td>
 +
    <td>TCGGGCTCTGGGAGCCCAGA </td>
 +
</tr>
 +
<tr class="tableunevengrnbl">
 +
    <td>EPO_M1</td>
 +
    <td>Targeting EPO exon-exon junction 2 with 4 mismatches</td>
 +
    <td>Fusion Protein</td>
 +
    <td></td>
 +
</tr>
 +
<tr class="tableevengrnbl">
 +
    <td>EPO_M2</td>
 +
    <td>Targeting EPO exon-exon junction 2 with 7 mismatches</td>
 +
    <td>Fusion Protein</td>
 +
    <td> GCACCCGGTGGTAATGTTTT </td>
 +
</tr>
 +
<tr class="tableunevengrnbl">
 +
    <td>EPO_M3</td>
 +
    <td>Targeting EPO exon-exon junction 2 with 3 mismatches</td>
 +
    <td>Fusion Protein</td>
 +
    <td> GCACCCGGTCGTGATATTCT </td>
 +
</tr>
 +
<tr class="tableevengrnbl">
 +
    <td>EPO_M4</td>
 +
    <td>Targeting EPO exon-exon junction 2 with 3 mismatches</td>
 +
    <td>Fusion Protein</td>
 +
    <td> ACAGCCCGTCGTAATGTTTT </td>
 +
</tr>
 +
<tr class="tableunevengrnbl">
 +
    <td>EPO_M5</td>
 +
    <td>Targeting EPO exon-exon junction 2 with 3 mismatches</td>
 +
    <td>Fusion Protein</td>
 +
    <td> GCAGCCCGTGGTGATATTTT </td>
 +
</tr>
 +
</table>
 +
 
 +
      <div class="spcmkr" id="adapters"></div>
 +
      <h1 class="grnbl">Adapters</h1>
 +
<table>
 +
  <tr class="tableheadergrnbl">
 +
    <th class="tableheadergrnbl">ID</th>
 +
    <th class="tableheadergrnbl">Name</th>
 +
    <th class="tableheadergrnbl">Module</th>
 +
    <th class="tableheadergrnbl">Sequence (dsDNA)</th>
 +
  </tr>
 
   </tr>
 
   </tr>
 
   <tr class="tableunevengrnbl">
 
   <tr class="tableunevengrnbl">
−
     <td>130</td>
+
     <td>036 <br>037</td>
−
     <td>SeqTim_08</td>
+
     <td width="15%">Adapter DNA short 1</td>
−
     <td>Sequencing</td>
+
     <td width="10%">Fusion Protein</td>
−
     <td>aatagactggatggaggcggCTGGGCTCCCAGAGCCCGAA</td>
+
<td>CTAGCTGTCTCTTATACACATCTATTGGCGAAATGGATGAACTGTTTACCATGC<br>GATCGACAGAGAATATGTGTAGATAACCGCTTTACCTACTTGACAAATGGTACG</td>
 +
  </tr>
 +
  <tr class="tableevengrnbl">
 +
    <td>062 <br> 063</td>
 +
    <td width="15%">Adapter DNA short 2</td>
 +
    <td width="10%">Fusion Protein</td>
 +
    <td>CTGTCTCTTATACACATCTATTGGCGAAATGGATGAACTGTTTACCATGC<br>GACAGAGAATATGTGTAGATAACCGCTTTACCTACTTGACAAATGGTACG</td>
 +
  </tr>
 +
  <tr class="tableunevengrnbl">
 +
    <td>087 <br>063</td>
 +
    <td width="15%">Adapter DNA labelled</td>
 +
    <td width="10%">Fusion Protein</td>
 +
<td>P-CTGTCTCTTATACACATCT<br>&ensp;&ensp;GACAGAGAATATGTGTAGATAACCGCTTTACCTACTTGACAAATGGTACG</td>
 +
  </tr>
 +
<tr class="tableevengrnbl">
 +
    <td>111<br>112</td>
 +
    <td width="15%">Adapter Sequencing</td>
 +
     <td width="10%">Sequencing</td>
 +
    <td>P-CTGTCTCTTATACACATCTATGCGCTTCGAA<br>&ensp;&ensp;GACAGAGAATATGTGTAGATACGCGAAGCT</td>
 +
  </tr>
 +
  <tr class="tableunevengrnbl">
 +
    <td>111<br>113</td>
 +
    <td width="15%">Adapter Sequencing</td>
 +
    <td width="10%">Sequencing</td>
 +
<td>P-CTGTCTCTTATACACATCTATGCGCTTCGAA<br>&ensp;&ensp;GACAGAGAATATGTGTAGATACGCGAAGCT-P</td>
 
   </tr>
 
   </tr>
 
</table>
 
</table>
 +
 
</div>
 
</div>
  

Latest revision as of 02:11, 18 October 2018

partssequences

Primers

ID Name Module Sequence (5' to 3')
001 fw_dxCas9 Fusion Protein atataGCGGCCGCtatggacaagaagtactccat
002 rv_dxCas9 Fusion Protein tatGGTACCttatGGCCGGCCcaccttcctcttcttcttgg
003 fw_dxCas9_mut_EcoRI Fusion Protein P-gcgaattttccaaaagagtgatcc
004 rv_dxCas9_mut_EcoRI Fusion Protein P-ttatttgctcgatgatctcatcaagg
005 fw_Tn5_afterC Fusion Protein tataGGCCGGCCtAAACTGGGCGGCGGCGCGCCGGCGGTGGGCGGCGGCCCGAAAGCGGCGGATAAAatgattaccagtgcactgcatc
006 rv_Tn5_afterC Fusion Protein tataGGTACCttagattttaatgccctgcgcca
007 fw_Tn5_beforeC Fusion Protein tataGAATTCtatgattaccagtgcactgcatc
008 rv_Tn5_beforeC Fusion Protein tataGCGGCCGCTTTATCCGCCGCTTTCGGGCCGCCGCCCACCGCCGGCGCGCCGCCGCCCAGTTTgattttaatgccctgcgcca
009 rv_dxCas9_mut1_GA Fusion Protein cattactaaagatctcttgcaggtagca
010 fw_dxCas9_mut1_GA Fusion Protein gctacctgcaagagatctttagtaatg
011 rv_dxCas9_mut2_GA Fusion Protein gaccttaacggtttgcagtattcc
012 fw_dxCas9_mut2_GA Fusion Protein ggaatactgcaaaccgttaagg
013 rv_dxCas9_mut3_GA Fusion Protein ccgttttgcaggtagtacag
014 fw_dxCas9_mut3_GA Fusion Protein ctgtactacctgcaaaacgg
015 rv_dxCas9_mut4_GA Fusion Protein tcgttacctttttgcagcac
016 fw_dxCas9_mut4_GA Fusion Protein tgctgcaaaaaggtaacgag
017 rv_dxCas9_mut5_GA Fusion Protein tacttgaaggctgccggc
018 fw_dxCas9_mut_GA Fusion Protein gccggcagccttcaag
019 fw_dxCas9_mut1_BL Fusion Protein P-gctacctgcaagagatctttagtaatg
020 rv_dxCas9_mut1_BL Fusion Protein P-agatccgattctttctgcgg
021 fw_dxCas9_mut2_BL Fusion Protein P-ggaatactgcaaaccgttaagg
022 rv_dxCas9_mut2_BL Fusion Protein P-ctttttgatagctgggctacct
023 fw_dxCas9_mut3_BL Fusion Protein P-ctgtactacctgcaaaacgg
024 rv_dxCas9_mut3_BL Fusion Protein P-gtagagcttctcattctgaagc
025 fw_dxCas9_mut4_BL Fusion Protein P-ctgcaaaaaggtaacgagctg
026 rv_dxCas9_mut4_BL Fusion Protein P-cacgcccgcactagc
027 fw_dxCas9_mut5_BL Fusion Protein P-gccggcagccttcaag
028 rv_dxCas9_mut5_BL Fusion Protein P-gcgcccaagttggtca
029 fw_T7_promoter General TAATACGACTCACTATAGGG
030 rv_T7_promoter General GCTAGTTATTGCTCAGCGG
031 VF2 General tgccacctgacgtctaagaa
032 VR General attaccgcctttgagtgagc
033 fw_sgRNA_1 Fusion Protein aagcTAATACGACTCACTATAGGGGAGGCCGAGAATATCA
034 rv_sgRNA_1 Fusion Protein AAAAGCACCGACTCGGTGCCACTT
035 fw_sgRNA_2 Fusion Protein aagcTAATACGACTCACTATAGGACAGCCCGTCGTGATATTCTGTTTTAGAGCTAGAAATAG
036 fw_adTn5_1 Fusion Protein CTAGCTGTCTCTTATACACATCTATTGGCGAAATGGATGAACTGTTTACCATGC
037 rv_adTn5_1 Fusion Protein GCATGGTAAACAGTTCATCCATTTCGCCAATAGATGTGTATAAGAGACAGCTAG
038 fw_1_AUpart d-AuNPs GATCGAATTCGCGGCCGCTTC
039 rv_1_AUpart d-AuNPs CGATTCTGCAGCGGCCGCTAC
040 fw_2_AUpart d-AuNPs GGAGGCCGAGAATATCACGA
041 rv_2_AUpart d-AuNPs TTGAGATCGTTTTGGTCTGC
042 fw_3_AUpart d-AuNPs CAGGTCGACAAGCTTGCG
043 fw_dCas9 Fusion Protein atataGCGGCCGCtatggataagaaatactcaataggcttagc
044 rv_dCas9 Fusion Protein tatGGTACCttatGGCCGGCCgtcacctcctagctgactc
045 fw_1_Tn5-L-dxCas9_Gblock Fusion Protein ACCATGGGCAGCAGC
046 rv_1_Tn5-L-dxCas9_Gblock Fusion Protein GTAGGGTATCCGAAATGTGAGGATTTTC
047 fw_2_Tn5-L-dxCas9_Gblock Fusion Protein GGGAAAAGATTGAGAAAATCCTCACATTTCG
048 rv_2_Tn5-L-dxCas9_Gblock Fusion Protein TGGCGTTCAAATTTCGCAGC
049 fw_pACYC-Duet_Backbone Fusion Protein GGTACCCTCGAGTCTGG
050 rv_pACYC-Duet_Backbone Fusion Protein GAATTCGGATCCTGGCTG
051 fw_BB_pSB1C3 BioBrick TACTAGTAGCGGCCGCTGC
052 rv_BB_pSB1C3 BioBrick CTAGAAGCGGCCGCGA
053 rv_BB_pSB1C3_extraNuc BioBrick CTCTAGAAGCGGCCGCGA
054 fw_BB_Tn5 BioBrick GCTAAGGATGATTTCTGGAATTCGCGGCCGCTTCTAGatgattaccagtgcactgcatcg
055 rv_BB_Tn5 BioBrick CCTTTTTTGCCGGACTGCAGCGGCCGCTACTAGTAttagattttaatgccctgcgccatc
056 fw_BB_dxCas9 BioBrick GCTAAGGATGATTTCTGGAATTCGCGGCCGCTTCTAGatggacaagaagtactccattgg
057 rv_BB_dxCas9 BioBrick CTTGCCCTTTTTTGCCGGACTGCAGCGGCCGCTACTAGTAttatggccggcccac
058 fw_BB_Linker BioBrick CGCTAAGGATGATTTCTGGAATTCGCGGCCGCTTCTAGAGGGCCGGCCtAAACTGG
059 rv_BB_Linker BioBrick CTTTTTTGCCGGACTGCAGCGGCCGCTACTAGTATTTATCCGCCGCTTTCGGGCCGCCGC
060 fw_BB_T7p BioBrick ATGATTTCTGGAATTCGCGGCCGCTTCTAGAGTAATACGACTCACTATAGGGGAATTGTG
061 rv_BB_T7p BioBrick TTGCCCTTTTTTGCCGGACTGCAGCGGCCGCTACTAGTAGCTAGTTATTGCTCAGCGGTG
062 fw_adTn5_2 Fusion Protein CTGTCTCTTATACACATCTATTGGCGAAATGGATGAACTGTTTACCATGC
063 rv_adTn5_2 Fusion Protein GCATGGTAAACAGTTCATCCATTTCGCCAATAGATGTGTATAAGAGACAG
064 rv_adTn5_label Fusion Protein Cy-GCATGGTAAACAGTTCATCCATTTCGCCAATAGATGTGTATAAGAGACAG
065 fw_1_AUpart d-AuNPs Cy-GATCGAATTCGCGGCCGCTTC
066 fw_bovine_albumin Sample Preparation TTGTTTCAACTCAAACAGCCTT
067 rv_bovine_albumin Sample Preparation AGAATCCCCATGGACAGAGA
068 fw_vectorxcas_spike Sample Preparation AGTAGCGGCCGCTGCAGaaggaagaggctgcaatctgtggc
069 rv_vectorxcas_spike Sample Preparation AGAAGCGGCCGCGAATTCcacacaagcagggagcagatactgg
070 fw_epo_spike Sample Preparation tgctccctgcttgtgtgGAATTCGCGGCCGCTTCT
071 rv_epo_spike Sample Preparation gattgcagcctcttccttCTGCAGCGGCCGCTAC
072 fw_epo_frag Sample Preparation GCCTCCCAGTCCTGGGCG
073 rv_epo_frag Sample Preparation GCAGTTGCAGGGGCTCCCAC
074 fw_epo_check Sample Preparation CCTGGAGAGGTACCTCTTGGAGGC
075 rv_epo_check Sample Preparation GCCCGACCTCCATCCTCTTCCAG
076 rv_adKan150 Fusion Protein catcctatggaactgcctcggtgagttttctccttc
077 rv_adKan300 Fusion Protein gaaatgcataagcttttgccattctcaccggattc
078 rv_adKan800 Fusion Protein gagccatattcaacgggaaacgtcttgctcc
079 fw_3_dxCas9-L-Tn5_Gblock Fusion Protein agaaataattttgtttaactttaataaggagatataccatgggc
080 rv_3_dxCas9-L-Tn5_Gblock Fusion Protein CTCGAATCAGTTTGTCATTTTCATCGTACTTG
081 fw_4_dxCas9-L-Tn5_Gblock Fusion Protein CCCAAATTCTCGATTCACGCATG
082 rv_4_dxCas9-L-Tn5_Gblock Fusion Protein tttagaggccccaaggggttatg
083 fw_2pACYC-Duet_Backbone Fusion Protein CTGCTGCCACCGCTG
084 rv_2pACYC-Duet_Backbone Fusion Protein GCTGCTGCCCATGGTATATC
085 fw_gblock1_mut_EcoRI Fusion Protein CAGGATCCGAATACTATGATTACC
086 rv_gblock1_mut_EcoRI Fusion Protein GGTAATCATAGTATTCGGATCCTG
087 fw_adTn5_Phos Fusion Protein P-CTGTCTCTTATACACATCT
088 fw_1_Tn5-dxCas9_Gblock_option2 Fusion Protein accatgggcagcagccatcaccatcatcaccacagcc
089 rv_1_Tn5-dxCas9_Gblock_option2 Fusion Protein cagggaaaagattgagaaaatcctcacatttcggataccctac
090 rv_BB_dxCas9_2 BioBrick CTGCAGCGGCCGCTACTAGTAttatGGCCGGCCcaccttcctcttcttcttg
091 fw_big_bovine_alb Sample Preparation CCCCCGTATCTGTCATTTCTTT
092 rv_big_bovine_alb Sample Preparation GGCATGGCAACCCACTGC
093 fw_dxcas_BL_bb BioBrick P-TACTAGTAGCGGCCGCTGCAGTCCGG
094 rv_dxcas_BL_bb BioBrick P-ttacaccttcctcttcttcttggggtcagccct
095 EPO-2 d-AuNPs TCCTGTCCCTGCTGTCGCTC
096 EPO-3 d-AuNPs GCCTGGAAGAGGATGGAGGT
097 EPO-4 d-AuNPs CTGCATGTGGATAAAGCCGT
098 EPO-5 d-AuNPs CGAACAATCACTGCTGACAC
099 fw_BB_sgRNA_EPO1 BioBrick gaattcgcggccgcttctagagGGAGGCCGAGAATATCAC
100 fw_BB_sgRNA_EPO2 BioBrick gaattcgcggccgcttctagagACAGCCCGTCGTGATATTCT
101 fw_BB_T7_sgRNA BioBrick gaattcgcggccgcttctagagaagcTAATACGACTCACTATAGG
102 rv_BB_sgRNA BioBrick ctgcagcggccgctactagtaGCACCGACTCGGTGCCAC
103 SeqTim_01 Sequencing GATATGAATAAATTGCAGTTTGTCGGGCAGCAGGCCGTAGA
104 SeqTim_02 Sequencing CATCATTGGCAACGCTACCCTCCATCCTCTTCCAGGCAT
105 SeqTim_03 Sequencing TCTACGGCCTGCTGCCCGACAAACTGCAATTTATTCATATC
106 SeqTim_04 Sequencing ATGCCTGGAAGAGGATGGAGGGTAGCGTTGCCAATGATG
107 SeqTim_05 Sequencing TTCGGGCTCTGGGAGCCCAGccgcctccatccagtctatt
108 SeqTim_06 Sequencing GGAGGGGAGATGGCTTCCTTgaatgaagccataccaaacg
109 SeqTim_07 Sequencing cgtttggtatggcttcattcAAGGAAGCCATCTCCCCTCC
110 SeqTim_08 Sequencing aatagactggatggaggcggCTGGGCTCCCAGAGCCCGAA
111 SeqTim_10 Sequencing P-CTGTCTCTTATACACATCTATGCGCTTCGAA
112 SeqTim_11 Sequencing AGCTTCGCGTATCTACACATATTCTCTGTC
113 SeqTim_12 Sequencing P-AGCTTCGCGTATCTACACATATTCTCTGTC
IV001 fw_IV1 In Vivo CCCTGAACCGACGACCGG
IV002 rv_IV1 In Vivo GCAGTGTGACCGTGTGCTTC
IV003 fw_IV2 In Vivo CTGAAACCTCAGGCATTTGAGAAGC
IV004 rv_IV2 In Vivo GAAATTCGAAAGCAAATTCGACCCGG
IV005 fw_KanR In Vivo CTAGCTGTCTCTTATACACATCTTTAGAAAAACTCATCGAGCATCAAATG
IV006 rv_KanR In Vivo GACTCTGTCTCTTATACACATCTATGAGCCATATTCAACGGG
IV007 fw_diagnostic In Vivo CCGGTAATAATCCACAGCAG
IV008 rv_diagnostic In Vivo CCAGATTCAGACAGCCAATC
IV009 fw_KanRCassetteME In Vivo CTAGCTGTCTCTTATACACATCTTAAcTAAcTAAcagctcgagtcccgtcaag
IV010 rv_KanRCassetteME In Vivo CTAGCTGTCTCTTATACACATCTTAAcTAAcTAAcaaagccacgttgtgtctc
IV011 fw_KanRCassette In Vivo TAAcTAAcTAAcagctcgagtcccgtc
IV012 rv_KanRCassette In Vivo TAAcTAAcTAAcaaagccacgttgtgtctc
IV013 fw_KanRCassetteME In Vivo cttggaCTGTCTCTTATACACATCTgacagctcgagtcccgtc
IV014 rv_KanRCassetteME In Vivo tgtcatCTGTCTCTTATACACATCTattcaacaaagccacgttgtgtctc
IV015 fw_KanRCassette In Vivo ctgacagctcgagtcccgtc
IV016 rv_KanRCassette In Vivo attcaacaaagccacgttgtgtctc
IV017 fw_KanRMEBiobrick BioBrick gaattcgcggccgcttctagagcttggaCTGTCTCTTATACACATCTgacag
IV018 rv_KanRMEBiobrick BioBrick tactagtagcggccgctgcagtgtcatCTGTCTCTTATACACATCTattcaacaaagc
IV019 rv_KanR internal BioBrick gcagtttcatttgatgctcgatgag
IV020 fw_KanR internal BioBrick ggctcataacaccccttgtattactg
IV021 fw target seq LacZ In Vivo TCGCACAGCGTGTACCACAG
IV022 rv target seq LacZ In Vivo CTGTGGTACACGCTGTGCG
IV023 fw_pSB1C3ori BioBrick GCAAGCAGCAGATTACGCG

ssDNAp

ID Name Module Sequence (5' to 3')
001 ssDNAp EPO 1 dAuNPs GGAGGCCGAGAATATCACGA
002 ssDNAp EPO 2 dAuNPs TCCTGTCCCTGCTGTCGCTC
003 ssDNAp EPO 3 dAuNPs GCCTGGAAGAGGATGGAGGT
004 ssDNAp EPO 4 dAuNPs CTGCATGTGGATAAAGCCGT
005 ssDNAp EPO 5 dAuNPs CGAACAATCACTGCTGACAC

sgRNA

ID Name Module Sequence (5' to 3')
001 sgRNA EPO 1 Fusion Protein aagcTAATACGACTCACTATAGGGGAGGCCGAGAATATCACGAGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTT
002 sgRNA EPO 2 Fusion Protein TAATACGACTCACTATAGGACAGCCCGTCGTGATATTCTGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGC
EPO_J1.1 Targeting EPO exon-exon junction 1, version 1 Fusion Protein GGGTGCACGAATGTCCTGCC
EPO_J1.2 Targeting EPO exon-exon junction 1, version 2 Fusion Protein ACGAATGTCCTGCCTGGCTG
EPO_J2.1 Targeting EPO exon-exon junction 2, version 1 Fusion Protein GGAGGCCGAGAATATCACGA
EPO_J.2.2 Targeting EPO exon-exon junction 2, version 2 Fusion Protein ACAGCCCGTCGTGATATTCT
EPO_J2.3 Targeting EPO exon-exon junction 2, version 3 Fusion Protein GAGGCCGAGAATATCACGAC
EPO_J3.1 Targeting EPO exon-exon junction 2, version 2 Fusion Protein CCTGGAAGAGGATGGAGGTC
EPO_J3.2 Targeting EPO exon-exon junction 3, version 1 Fusion Protein GAGGATGGAGGTCGGGCAGC
EPO_J3.1 Targeting EPO exon-exon junction 3, version 2 Fusion Protein CCTGGAAGAGGATGGAGGTC
EPO_J4.1 Targeting EPO exon-exon junction 4, version 1 Fusion Protein AGGGGAGATGGCTTCCTTCT
EPO_J4.2 Targeting EPO exon-exon junction 4, version 2 Fusion Protein TCGGGCTCTGGGAGCCCAGA
EPO_M1 Targeting EPO exon-exon junction 2 with 4 mismatches Fusion Protein
EPO_M2 Targeting EPO exon-exon junction 2 with 7 mismatches Fusion Protein GCACCCGGTGGTAATGTTTT
EPO_M3 Targeting EPO exon-exon junction 2 with 3 mismatches Fusion Protein GCACCCGGTCGTGATATTCT
EPO_M4 Targeting EPO exon-exon junction 2 with 3 mismatches Fusion Protein ACAGCCCGTCGTAATGTTTT
EPO_M5 Targeting EPO exon-exon junction 2 with 3 mismatches Fusion Protein GCAGCCCGTGGTGATATTTT

Adapters

ID Name Module Sequence (dsDNA)
036
037		 Adapter DNA short 1 Fusion Protein CTAGCTGTCTCTTATACACATCTATTGGCGAAATGGATGAACTGTTTACCATGC
GATCGACAGAGAATATGTGTAGATAACCGCTTTACCTACTTGACAAATGGTACG
062
063		 Adapter DNA short 2 Fusion Protein CTGTCTCTTATACACATCTATTGGCGAAATGGATGAACTGTTTACCATGC
GACAGAGAATATGTGTAGATAACCGCTTTACCTACTTGACAAATGGTACG
087
063		 Adapter DNA labelled Fusion Protein P-CTGTCTCTTATACACATCT
  GACAGAGAATATGTGTAGATAACCGCTTTACCTACTTGACAAATGGTACG
111
112		 Adapter Sequencing Sequencing P-CTGTCTCTTATACACATCTATGCGCTTCGAA
  GACAGAGAATATGTGTAGATACGCGAAGCT
111
113		 Adapter Sequencing Sequencing P-CTGTCTCTTATACACATCTATGCGCTTCGAA
  GACAGAGAATATGTGTAGATACGCGAAGCT-P