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50 51 <title>piRNAi app</title>
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54 55<link rel="stylesheet" type="text/css" href="__assets__/shiny-server.css"/> 56 57</head> 58<body> 59 <div class="container-fluid"> 60 <style type="text/css">.js-irs-none .irs-single, .js-irs-none .irs-bar-edge, .js-irs-none .irs-bar { 61 background: transparent; 62 border-top-color: transparent; 63 border-bottom-color: transparent; 64 border-left-color: transparent; 65 border-right-color: transparent} 66 .navbar-default .navbar-brand:hover {color: #ffffff;} 67 </style> 68 <style type="text/css">#AdvancedFragment {white-space: pre-wrap;}</style> 69 <style type="text/css">#SimpleFragment {white-space: pre-wrap;}</style> 70 <style type="text/css">#piBoxes .form-group {margin-bottom: 0px; margin-top: 0px;}</style> 71 <style type="text/css"> 72 table { 73 font-family: arial, sans-serif; 74 border-collapse: collapse; 75 width: 100%; 76} 77 78td, th { 79 border: 1px solid #dddddd; 80 text-align: left; 81 padding: 8px; 82} 83 84tr:nth-child(even) { 85 background-color: #dddddd; 86} 87 </style> 88 <nav class="navbar navbar-default navbar-static-top" role="navigation"> 89 <div class="container-fluid"> 90 <div class="navbar-header"> 91 <span class="navbar-brand"> 92 <a id="link_to_tabpanel_title" href="#" class="action-button"><b>piRNAi</b></a> 93 </span> 94 </div> 95 <ul class="nav navbar-nav shiny-tab-input" id="panels" data-tabsetid="3152"> 96 <li class="active"> 97 <a href="#tab-3152-1" data-toggle="tab" data-value="Designer">Designer</a> 98 </li> 99 <li> 100 <a href="#tab-3152-2" data-toggle="tab" data-value="Downloads">Downloads</a> 101 </li> 102 <li> 103 <a href="#tab-3152-3" data-toggle="tab" data-value="About">About</a> 104 </li> 105 </ul> 106 </div> 107 </nav> 108 <div class="container-fluid"> 109 <div class="tab-content" data-tabsetid="3152"> 110 <div class="tab-pane active" data-value="Designer" id="tab-3152-1"> 111 <div class="col-sm-8"> 112 <h2>Design piRNAi fragments</h2> 113 <h4>Target <i>C. elegans</i> and <i>C. briggsae</i> genes</h4> 114 <div class="tabbable"> 115 <ul class="nav nav-tabs" data-tabsetid="1370"> 116 <li class="active"> 117 <a href="#tab-1370-1" data-toggle="tab" data-value="Simple">Simple</a> 118 </li> 119 <li> 120 <a href="#tab-1370-2" data-toggle="tab" data-value="Advanced">Advanced</a> 121 </li> 122 </ul> 123 <div class="tab-content" data-tabsetid="1370"> 124 <div class="tab-pane active" data-value="Simple" id="tab-1370-1"> 125 <br/> 126 <div class="form-group shiny-input-container"> 127 <label class="control-label" for="geneinput">Target gene</label> 128 <textarea id="geneinput" class="form-control" placeholder="WormbaseID, transcript or gene name" style=" resize: none;" rows="1"></textarea> 129 </div> 130 <button id="actiongenesearch" type="button" class="btn btn-default action-button">Search</button> 131 <hr/> 132 <div id="DesignControls" class="shiny-html-output"></div> 133 <hr/> 134 <pre id="ErrorMessage" class="shiny-text-output noplaceholder"></pre> 135 <div id="SelPiTabSummary" class="shiny-html-output"></div> 136 <div id="SelPiTab" class="shiny-html-output"></div> 137 <pre id="SimpleFragment" class="shiny-text-output noplaceholder"></pre> 138 <div id="RefMesSim" class="shiny-html-output"></div> 139 <div id="downloadseq" class="shiny-html-output"></div> 140 </div> 141 <div class="tab-pane" data-value="Advanced" id="tab-1370-2"> 142 <h3>Select individual synthetic guide piRNAs</h3> 143 <div class="row"> 144 <div id="clustercon" style="width: 100%;" class="form-group shiny-input-radiogroup shiny-input-container shiny-input-container-inline"> 145 <label class="control-label" for="clustercon">Select piRNA cluster 146 [<a href="" onclick="$('#explain_cluster_adv').toggle(); return false;">info</a>] 147 </label> 148 <div class="shiny-options-group"> 149 <label class="radio-inline"> 150 <input type="radio" name="clustercon" value="1" checked="checked"/>
151 <span>Standard piRNA transgene (Cluster<sub>E</sub>, six sg-piRNAs)</span> 152 </label> 153 <label class="radio-inline"> 154 <input type="radio" name="clustercon" value="2"/> 155 <span>Cluster<sub>G</sub> (six sg-piRNAs)</span> 156 </label> 157 <label class="radio-inline"> 158 <input type="radio" name="clustercon" value="3"/> 159 <span>Cluster<sub>O</sub> (seven sg-piRNAs)</span> 160 </label> 161 <label class="radio-inline"> 162 <input type="radio" name="clustercon" value="4"/> 163 <span>Cluster<sub>F</sub> (eight sg-piRNAs)</span> 164 </label> 165 </div> 166 </div> 167 168 <p align="justify"><div class="explain" style="display: none" id="explain_cluster_adv"> 169 We recommend using the standard piRNAi Cluster<sub>E</sub> (centered on the <i>21ur-1224</i> piRNA loci). <b>Note:</b> Cluster<sub>O</sub> and Cluster<sub>F</sub> were tested with six sg-piRNAs but can accomodate additional sg-piRNAs, which may improve silencing. 170 </div></p> 171 172 <div data-display-if="input.clustercon==1" data-ns-prefix=""> 173 <div class="col-sm-4"> 174 <div id="piBoxes" class="my_class"> 175 <div class="form-group shiny-input-container"> 176 <label class="control-label" for="piRNAseq1_1"></label> 177 <textarea id="piRNAseq1_1" class="form-control" placeholder="sg-piRNA 1" style=" resize: none;" rows="1" cols="21"></textarea> 178 </div> 179 <div class="form-group shiny-input-container"> 180 <label class="control-label" for="piRNAseq2_1"></label> 181 <textarea id="piRNAseq2_1" class="form-control" placeholder="sg-piRNA 2" style=" resize: none;" rows="1" cols="21"></textarea> 182 </div> 183 <div class="form-group shiny-input-container"> 184 <label class="control-label" for="piRNAseq3_1"></label> 185 <textarea id="piRNAseq3_1" class="form-control" placeholder="sg-piRNA 3" style=" resize: none;" rows="1" cols="21"></textarea> 186 </div> 187 <div class="form-group shiny-input-container"> 188 <label class="control-label" for="piRNAseq4_1"></label> 189 <textarea id="piRNAseq4_1" class="form-control" placeholder="sg-piRNA 4" style=" resize: none;" rows="1" cols="21"></textarea> 190 </div> 191 <div class="form-group shiny-input-container"> 192 <label class="control-label" for="piRNAseq5_1"></label> 193 <textarea id="piRNAseq5_1" class="form-control" placeholder="sg-piRNA 5" style=" resize: none;" rows="1" cols="21"></textarea> 194 </div> 195 <div class="form-group shiny-input-container"> 196 <label class="control-label" for="piRNAseq6_1"></label> 197 <textarea id="piRNAseq6_1" class="form-control" placeholder="sg-piRNA 6" style=" resize: none;" rows="1" cols="21"></textarea> 198 </div> 199 </div> 200 <br/> 201 </div> 202 </div> 203 <div data-display-if="input.clustercon==2" data-ns-prefix=""> 204 <div class="col-sm-4"> 205 <div id="piBoxes" class="my_class"> 206 <div class="form-group shiny-input-container"> 207 <label class="control-label" for="piRNAseq1_2"></label> 208 <textarea id="piRNAseq1_2" class="form-control" placeholder="sg-piRNA 1" style=" resize: none;
208" rows="1" cols="21"></textarea> 209 </div> 210 <div class="form-group shiny-input-container"> 211 <label class="control-label" for="piRNAseq2_2"></label> 212 <textarea id="piRNAseq2_2" class="form-control" placeholder="sg-piRNA 2" style=" resize: none;" rows="1" cols="21"></textarea> 213 </div> 214 <div class="form-group shiny-input-container"> 215 <label class="control-label" for="piRNAseq3_2"></label> 216 <textarea id="piRNAseq3_2" class="form-control" placeholder="sg-piRNA 3" style=" resize: none;" rows="1" cols="21"></textarea> 217 </div> 218 <div class="form-group shiny-input-container"> 219 <label class="control-label" for="piRNAseq4_2"></label> 220 <textarea id="piRNAseq4_2" class="form-control" placeholder="sg-piRNA 4" style=" resize: none;" rows="1" cols="21"></textarea> 221 </div> 222 <div class="form-group shiny-input-container"> 223 <label class="control-label" for="piRNAseq5_2"></label> 224 <textarea id="piRNAseq5_2" class="form-control" placeholder="sg-piRNA 5" style=" resize: none;" rows="1" cols="21"></textarea> 225 </div> 226 <div class="form-group shiny-input-container"> 227 <label class="control-label" for="piRNAseq6_2"></label> 228 <textarea id="piRNAseq6_2" class="form-control" placeholder="sg-piRNA 6" style=" resize: none;" rows="1" cols="21"></textarea> 229 </div> 230 </div> 231 <br/> 232 </div> 233 </div> 234 <div data-display-if="input.clustercon==3" data-ns-prefix=""> 235 <div class="col-sm-4"> 236 <div id="piBoxes" class="my_class"> 237 <div class="form-group shiny-input-container"> 238 <label class="control-label" for="piRNAseq1_3"></label> 239 <textarea id="piRNAseq1_3" class="form-control" placeholder="sg-piRNA 1" style=" resize: none;" rows="1" cols="21"></textarea> 240 </div> 241 <div class="form-group shiny-input-container"> 242 <label class="control-label" for="piRNAseq2_3"></label> 243 <textarea id="piRNAseq2_3" class="form-control" placeholder="sg-piRNA 2" style=" resize: none;" rows="1" cols="21"></textarea> 244 </div> 245 <div class="form-group shiny-input-container"> 246 <label class="control-label" for="piRNAseq3_3"></label> 247 <textarea id="piRNAseq3_3" class="form-control" placeholder="sg-piRNA 3" style=" resize: none;" rows="1" cols="21"></textarea> 248 </div> 249 <div class="form-group shiny-input-container"> 250 <label class="control-label" for="piRNAseq4_3"></label> 251 <textarea id="piRNAseq4_3" class="form-control" placeholder="sg-piRNA 4" style=" resize: none;" rows="1" cols="21"></textarea> 252 </div> 253 <div class="form-group shiny-input-container"> 254 <label class="control-label" for="piRNAseq5_3"></label> 255 <textarea id="piRNAseq5_3" class="form-control" placeholder="sg-piRNA 5" style=" resize: none;" rows="1" cols="21"></textarea> 256 </div> 257 <div class="form-group shiny-input-container"> 258 <label class="control-label" for="piRNAseq6_3"></label> 259 <textarea id="piRNAseq6_3" class="form-control" placeholder="sg-piRNA 6" style=" resize: none;
259" rows="1" cols="21"></textarea> 260 </div> 261 <div class="form-group shiny-input-container"> 262 <label class="control-label" for="piRNAseq7_3"></label> 263 <textarea id="piRNAseq7_3" class="form-control" placeholder="sg-piRNA 7" style=" resize: none;" rows="1" cols="21"></textarea> 264 </div> 265 </div> 266 <br/> 267 </div> 268 </div> 269 <div data-display-if="input.clustercon==4" data-ns-prefix=""> 270 <div class="col-sm-4"> 271 <div id="piBoxes" class="my_class"> 272 <div class="form-group shiny-input-container"> 273 <label class="control-label" for="piRNAseq1_4"></label> 274 <textarea id="piRNAseq1_4" class="form-control" placeholder="sg-piRNA 1" style=" resize: none;" rows="1" cols="21"></textarea> 275 </div> 276 <div class="form-group shiny-input-container"> 277 <label class="control-label" for="piRNAseq2_4"></label> 278 <textarea id="piRNAseq2_4" class="form-control" placeholder="sg-piRNA 2" style=" resize: none;" rows="1" cols="21"></textarea> 279 </div> 280 <div class="form-group shiny-input-container"> 281 <label class="control-label" for="piRNAseq3_4"></label> 282 <textarea id="piRNAseq3_4" class="form-control" placeholder="sg-piRNA 3" style=" resize: none;" rows="1" cols="21"></textarea> 283 </div> 284 <div class="form-group shiny-input-container"> 285 <label class="control-label" for="piRNAseq4_4"></label> 286 <textarea id="piRNAseq4_4" class="form-control" placeholder="sg-piRNA 4" style=" resize: none;" rows="1" cols="21"></textarea> 287 </div> 288 <div class="form-group shiny-input-container"> 289 <label class="control-label" for="piRNAseq5_4"></label> 290 <textarea id="piRNAseq5_4" class="form-control" placeholder="sg-piRNA 5" style=" resize: none;" rows="1" cols="21"></textarea> 291 </div> 292 <div class="form-group shiny-input-container"> 293 <label class="control-label" for="piRNAseq6_4"></label> 294 <textarea id="piRNAseq6_4" class="form-control" placeholder="sg-piRNA 6" style=" resize: none;" rows="1" cols="21"></textarea> 295 </div> 296 <div class="form-group shiny-input-container"> 297 <label class="control-label" for="piRNAseq7_4"></label> 298 <textarea id="piRNAseq7_4" class="form-control" placeholder="sg-piRNA 7" style=" resize: none;" rows="1" cols="21"></textarea> 299 </div> 300 <div class="form-group shiny-input-container"> 301 <label class="control-label" for="piRNAseq8_4"></label> 302 <textarea id="piRNAseq8_4" class="form-control" placeholder="sg-piRNA 8" style=" resize: none;" rows="1" cols="21"></textarea> 303 </div> 304 </div> 305 <br/> 306 </div> 307 </div> 308 <div data-display-if="input.clustercon==5" data-ns-prefix=""> 309 <div class="col-sm-4"> 310 <div id="piBoxes" class="my_class"> 311 <div class="form-group shiny-input-container"> 312 <label class="control-label" for="piRNAseq1_5"></label> 313 <textarea id="piRNAseq1_5" class="form-control" placeholder="sg-piRNA 1" style=" resize: none;" rows="1" cols="21"></textarea> 314 </div> 315 <div class="form-group shiny-input-container"> 316 <label class="control-label" for="piRNAseq2_5"></label> 317 <textarea id="piRNAseq2_5" class="form-control" placeholder="sg-piRNA 2" style=" resize: none;
317" rows="1" cols="21"></textarea> 318 </div> 319 <div class="form-group shiny-input-container"> 320 <label class="control-label" for="piRNAseq3_5"></label> 321 <textarea id="piRNAseq3_5" class="form-control" placeholder="sg-piRNA 3" style=" resize: none;" rows="1" cols="21"></textarea> 322 </div> 323 <div class="form-group shiny-input-container"> 324 <label class="control-label" for="piRNAseq4_5"></label> 325 <textarea id="piRNAseq4_5" class="form-control" placeholder="sg-piRNA 4" style=" resize: none;" rows="1" cols="21"></textarea> 326 </div> 327 <div class="form-group shiny-input-container"> 328 <label class="control-label" for="piRNAseq5_5"></label> 329 <textarea id="piRNAseq5_5" class="form-control" placeholder="sg-piRNA 5" style=" resize: none;" rows="1" cols="21"></textarea> 330 </div> 331 <div class="form-group shiny-input-container"> 332 <label class="control-label" for="piRNAseq6_5"></label> 333 <textarea id="piRNAseq6_5" class="form-control" placeholder="sg-piRNA 6" style=" resize: none;" rows="1" cols="21"></textarea> 334 </div> 335 <div class="form-group shiny-input-container"> 336 <label class="control-label" for="piRNAseq7_5"></label> 337 <textarea id="piRNAseq7_5" class="form-control" placeholder="sg-piRNA 7" style=" resize: none;" rows="1" cols="21"></textarea> 338 </div> 339 <div class="form-group shiny-input-container"> 340 <label class="control-label" for="piRNAseq8_5"></label> 341 <textarea id="piRNAseq8_5" class="form-control" placeholder="sg-piRNA 8" style=" resize: none;" rows="1" cols="21"></textarea> 342 </div> 343 </div> 344 <br/> 345 </div> 346 </div> 347 <div class="col-sm-8"> 348 <pre id="AdvancedFragment" class="shiny-text-output noplaceholder"></pre> 349 <div id="RefMesAdv" class="shiny-html-output"></div> 350 <div id="downloadconstruct" class="shiny-html-output"></div> 351 </div> 352 </div> 353 <div class="row"> 354 <div class="col-sm-2"> 355 <button id="actionclean" type="button" class="btn btn-default action-button">Reset</button> 356 </div> 357 <div class="col-sm-2"> 358 <button id="actionconstruct" type="button" class="btn btn-default action-button">Generate piRNAi cluster</button> 359 </div> 360 </div> 361 <pre id="AdvancedErrorMessage" class="shiny-text-output noplaceholder"></pre> 362 <hr/> 363 <div class="form-group shiny-input-container"> 364 <label class="control-label" for="Advancedgeneinput">Gene target</label> 365 <textarea id="Advancedgeneinput" class="form-control" placeholder="WormbaseID, transcript or gene name" style=" resize: none;" rows="1"></textarea> 366 </div> 367 <button id="actionAdvsearch" type="button" class="btn btn-default action-button">Search piRNAs</button> 368 <br/> 369 <br/> 370 <div class="form-group shiny-input-container"> 371 <label class="control-label" for="FluoInput"><b>Common fluorophore 372 [<a href="" onclick="$('#explain_n_fluo').toggle(); return false;">info</a>]</b></label> 373 <div> 374 <select id="FluoInput"><option value="ce-GFP (Froekjaer-Jensen lab)">ce-GFP (Froekjaer-Jensen lab)</option> 375<option value="ce-tagRFP (Froekjaer-Jensen lab)">ce-tagRFP (Froekjaer-Jensen lab)</option> 376<option value="GFP (Fire lab)">GFP (Fire lab)</option> 377<option value="mCherry (Oegema lab)">mCherry (Oegema lab)</option> 378<option value="mCherry (Seydoux lab)">mCherry (Seydoux lab)</option> 379<option value="mKate2 (Dickinson lab)">mKate2 (Dickinson lab)</option> 380<option value="mNeonGreen (Dickinson lab)">mNeonGreen (Dickinson lab)</option></select> 381
381<script type="application/json" data-for="FluoInput" data-nonempty="">{}</script>
381 382 </div> 383 </div> 384 385 <p align="justify"><div class="explain" style="display: none" id="explain_n_fluo"> 386 We have designed sg-piRNAs that specifically target common fluorophores used in <i>C. elegans</i> labs. Please see the Download tab for primary DNA sequences. 387 </div></p> 388 389 <button id="ActionFluoSearch" type="button" class="btn btn-default action-button">Show piRNAs</button> 390 <hr/> 391 <div id="AdvDesignControls" class="shiny-html-output"></div> 392 <hr/> 393 <div id="AllPiTab" style="width:100%; height:auto; " class="datatables html-widget html-widget-output"></div> 394 </div> 395 </div> 396 </div> 397 </div> 398 </div> 399 <div class="tab-pane" data-value="Downloads" id="tab-3152-2"> 400 <div class="col-sm-8"> 401 <h3>Tracks</h3> 402 <br>Bed tracks with <i>C. elegans</i> (WS270) guide-piRNAs for each specifity criteria. 403 404 <p align="justify"> 405 <a href="https://s3.eu-central-1.amazonaws.com/wormbuilder.dev/Downloads/piRNAi_dev/piRNAi_Cel_WS270.tar.gz">Download (307 MB)</a><br> 406 <br><h3>Sequences</h3> 407 <table> 408 <tr> 409 <th>Name</th> 410 <th>Lab</th> 411 <th>GenBank file (ApE annotations)</th> 412 </tr> 413 <tr> 414 <td>ce-GFP</td> 415 <td>Froekjaer-Jensen lab</td> 416 <td><a href="https://s3.eu-central-1.amazonaws.com/wormbuilder.dev/Downloads/piRNAi_dev/Apes/ce-GFP_AlJohani.ape">ce-gfp.gb</a></td> 417 </tr> 418 <tr> 419 <td>ce-tagRFP</td> 420 <td>Froekjaer-Jensen lab</td> 421 <td><a href="https://s3.eu-central-1.amazonaws.com/wormbuilder.dev/Downloads/piRNAi_dev/Apes/ce-TagRFP-T_AlJohani.ape">ce-tagRFP-T.gb</a></td> 422 </tr> 423 <tr> 424 <td>GFP</td> 425 <td>Fire lab</td> 426 <td><a href="https://s3.eu-central-1.amazonaws.com/wormbuilder.dev/Downloads/piRNAi_dev/Apes/gfp(S65C_Fire).ape">gfp(S65C).gb</a></td> 427 </tr> 428 <tr> 429 <td>mCherry</td> 430 <td>Oegema lab</td> 431 <td><a href="https://s3.eu-central-1.amazonaws.com/wormbuilder.dev/Downloads/piRNAi_dev/Apes/mCherry_Oegema.ape">mCherry(Oegema).gb</a></td> 432 </tr> 433 <tr> 434 <td>mCherry</td> 435 <td>Seydoux lab</td> 436 <td><a href="https://s3.eu-central-1.amazonaws.com/wormbuilder.dev/Downloads/piRNAi_dev/Apes/mCherry_Seydoux.ape">mCherry(Seydoux).gb</a></td> 437 </tr> 438 <tr> 439 <td>mKate2</td> 440 <td>Dickinson lab</td> 441 <td><a href="https://s3.eu-central-1.amazonaws.com/wormbuilder.dev/Downloads/piRNAi_dev/Apes/mKate2_Dickinson.ape">mKate2.gb</a></td> 442 </tr> 443 <tr> 444 <td>mNeonGreen</td> 445 <td>Dickinson lab</td> 446 <td><a href="https://s3.eu-central-1.amazonaws.com/wormbuilder.dev/Downloads/piRNAi_dev/Apes/mNeonGreen_Dickinson.ape">mNeonGreen.gb</a></td> 447 </tr> 448</table> 449 </p> 450 </div> 451 </div> 452 <div class="tab-pane" data-value="About" id="tab-3152-3"> 453 <div class="col-sm-8"> 454 <h3>The piRNA-based RNA interference app ("piRNAi")</h3> 455 <p align="justify"> 456 This website was generated via custom modified css/html code running in R via the shiny library. 457 <br>All the templates, libraries, and programs used to produce this site are under the MIT and GNU licenses. 458 <br>While the rationale behind the app is described in the background section, its implementation can be found at <a href="https://www.researchgate.net/profile/Amhed_Vargas_Velazquez">Amhed Missael Vargas Velazquez</a> | <a href="https://github.com/AmhedVargas">Github account</a></p> 459 <h3>The Laboratory of Synthetic Genome Biology</h3> 460 <p align="justify"> 461 The Laboratory of Synthetic Genome Biology is located in building 2 - level 3 (Ibn Al-Haytham â Above Spine) at King Abdullah University of Science and Technology (KAUST). 462 <br><i>Contact info</i>:<br>Christian-Froekjaer Jensen, Ph.D. 463 <br>Assistant Professor of Bioscience 464 <br>Laboratory of Synthetic Genome Biology 465 <br>
465Email: <a href="mailto:[email protected]">[email protected]</a> 466 </p> 467 </div> 468 </div> 469 </div> 470 </div> 471 <hr/> 472 <a href="http://www.wormbuilder.org/">Wormbuilder</a><br> 473 <a href="mailto:[email protected]">Contact us!</a> 474 </div> 475</body> 476</html>
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