Latest revision as of 22:51, 1 November 2017

<!DOCTYPE html> Coli Sapiens

iGEM Tokyo Tech

Transcriptome Analysis

Introduction

In our project, we worked on establishing an artificial cross-kingdom communication between human cells and bacteria. However, the cross-kingdom communication was not known well. Therefore, we first had to choose appropriate signaling molecules to establish it. We chose one of the AHL molecules, 3OC8HSL, as a signaling molecule from bacteria to human cells. This is because it can interact with only genetically engineered human cells (Read TraI Assay page). Next, we had to choose a signaling molecule from human cells to bacteria. Initially we had planned to use another AHL. However, we decided not to use AHLs as signal molecules from human cells to bacteria since AHLs cannot be synthesized by human cells due to lack of their materials [2]. Thus, we had to explore if there is a potential signaling molecule produced by human cells. To this end, E. coli cells were interacted with the supernatant of the medium which human cells were cultured. Then transcriptome analysis was conducted to observe if there were any differences in the gene expression in E. coli.

Summary

We checked the difference of transcription between E. coli in normal medium and E. coli in the medium which human cells were cultured. Surprisingly, there were no significant differences in almost all of the RNA expressions except for a couple of genes. The difference was only a little even for those genes.

Results

The 4318 genes were checked and malGcoding Maltose transport system permease protein MalG and malFcoding Maltose transport system permease protein MalF were transcribed about 1.7-fold. This excel file is the data of the transcriptome analysis. The value of E- FDR of the all genes was 1.

Click here to download the result data

Discussion

It is said that the difference is statistically significant if the value of E-FDR is 0.5 or less. Therefore, the results showed that most of the genes were not activated or repressed by substances derived from human cells. Two genes related to maltose metabolism were transcribed about 1.7-fold higher. This fact indicates that a substance like maltose was secreted from human cells. However, it was not proper for a signaling molecule because the activation rate was very low. Considering this result, no substances derived from human could be used as our ideal signaling molecule. Therefore, we had to explore another substance which works as a signaling molecule (Read AHK4 Assay page and Project page).

Appendix: Material and Method

Reference

[1] Foundational Platform for Mammalian Synthetic Biology, 2012 Noah Davidsohn et.al

[2] Multiple reference genomes and transcriptomes for Arabidopsis thaliana, 2011 Xiangchao Gan et.al

@@ Line 7: / Line 7: @@
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <link rel="stylesheet" href="main.css">
-<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Poppins">
 <style>
-body,h1,h2,h3,h4,h5 {font-family: "Poppins", sans-serif}
+body,h1,h2,h3,h4,h5 {font-family: "Arial", sans-serif}
 body {font-size:16px;}
 .w3-half img{margin-bottom:-6px;margin-top:16px;opacity:0.8;cursor:pointer}
@@ Line 15: / Line 14: @@
 </style>
 <body>
+<div id="loader-bg">
+  <div id="loader">
+    <div class="photo-show">
+    <img src="https://static.igem.org/mediawiki/2017/f/f4/T--TokyoTech--load_1.png" width="600">
+    <img src="https://static.igem.org/mediawiki/2017/4/43/T--TokyoTech--load_2.png" width="600">
+    </div>
+  </div>
+</div>
 <!-- Sidebar/menu -->
 <nav class="w3-sidebar w3-red w3-collapse w3-top w3-large w3-padding" style="z-index:3;width:300px;font-weight:bold;" id="mySidebar"><br>
    <a href="javascript:void(0)" onclick="w3_close()" class="w3-button w3-hide-large w3-display-topleft" style="width:100%;font-size:20px">Close Menu</a>
-   <div class="w3-container" style="margin-top: 20px;margin-bottom: 25px">
+   <div class="w3-container" style="margin-top: 20px;margin-bottom: 25px" id="wrap">
      <img src="https://static.igem.org/mediawiki/2017/a/a8/T--TokyoTech--logo_white_bright_10211603.png" style="width: 100%">
    </div>
-   <div style="padding-top: 15px; padding-left: 25px;">
+   <div style="padding-top: 15px; padding-left: 25px; id="wrap">
    <div id="contents" style="z-index: 10">
@@ Line 50: / Line 58: @@
      <label for="vmcb-d"><a>Experiment</a></label>
       <ul>
          <li>
          <input type="checkbox" id="vmcb-d1" />
-          <label for="vmcb-d1"><a style="text-align: center;">Bacteria to <br> Human Cells</a></label>
+        <label for="vmcb-d1"><a href="https://2017.igem.org/Team:TokyoTech/Experiment/Overview" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white" style="text-align: center;">Overview</a></label>
+        </li>
+        <li style="padding-bottom: 10px; padding-top: 5px">
+        <input type="checkbox" id="vmcb-d2" />
+          <label for="vmcb-d2"><a style="text-align: center;">Bacteria to <br>Human Cells ▼</a></label>
              <ul>
                <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Experiment/TraI_Assay" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">TraI Assay</a></li>
-               <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Experiment/TraI_Improvement" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">TraI <br> Impovement</a></li>
+               <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Experiment/TraI_Improvement" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">TraI Improvement <br>Assay</a></li>
-               <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Experiment/TraR_Reporter_Assay" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white" >TraR Reporter <br> Assay</a></li>
+               <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Experiment/TraR_Reporter_Assay" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white" >TraR Reporter <br>Assay</a></li>
-               <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Experiment/Transcriptome_Analysis" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Transcriptome <br> Analysis</a></li>
+               <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Experiment/Transcriptome_Analysis" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Transcriptome <br>Analysis</a></li>
-              <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Experiment/C8_Toxicity" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">C8 Toxicity <br> Assay</a></li>
+               <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Experiment/Chimeric_Transcription_Factor" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Chimeric <br> Transcription <br> Factor Assay</a></li>
-               <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Experiment/Chimeric_Transcription_Factor" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Chimeric <br> Transcription <br> Factor</a></li>
              </ul>
        </li>
-       <li><input type="checkbox" id="vmcb-d2" />
-     <label for="vmcb-d2"><a style="text-align: center;">Human Cells to Bacteria</a></label>
+       <li style="padding-bottom: 3px">
+      <input type="checkbox" id="vmcb-d3" />
+     <label for="vmcb-d3"><a style="text-align: center;">Human Cells to <br>Bacteria ▼</a></label>
          <ul>
            <li><a href="https://2017.igem.org/Team:TokyoTech/Experiment/AHK4_Assay" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">AHK4 Assay</a></li>
            </ul>
+        </li>
+        <li>
+        <input type="checkbox" id="vmcb-d4" />
+    <label for="vmcb-d4"><a href="https://2017.igem.org/Team:TokyoTech/InterLab" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white" style="text-align: center;">InterLab</a></label>
          </li>
      </ul>
@@ Line 83: / Line 103: @@
      <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/HP" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Overview</a></li>
      <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/HP/Silver" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Silver</a></li>
-     <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/HP/Gold_Integrated" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Integrated <br> Human Practice</a></li>
+     <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/HP/Gold_Integrated" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Gold (Integrated)</a></li>
+    <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Demonstrate" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Demonstrate</a></li>
      <li style="text-align: center;"><a href="https://2017.igem.org/Team:TokyoTech/Collaborations" onclick="w3_close()" class="w3-bar-item w3-button w3-hover-white">Collaborations</a></li>
      </ul>
@@ Line 102: / Line 123: @@
    </div>
 </nav>
 <!-- Top menu on small screens -->
 <header class="w3-container w3-top w3-hide-large w3-red w3-xlarge w3-padding">
@@ Line 122: / Line 144: @@
      <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Introduction</b></h1><!-- 小見出し -->
      <hr style="width:50px;border:5px solid red" class="w3-round">
-    <p style="font-family: Poppins;font-size: 16px"><p style="text-indent:1em"> In our project, we worked on establishing an artificial inter-kingdom communication between human cells and bacteria. However, the inter-kingdom communication was not known well. Therefore,  we first had to choose appropriate signaling molecules to establish it. We chose one of the AHL molecules, 3OC8HSL, as a signaling molecule from bacteria to human cells. This is because it can interact with only genetically engineered human cells [1, read <a href="https://2017.igem.org/Team:TokyoTech/Experiment/TraI_Assay">TraI Assay</a> page]. Next, we had to choose a signaling molecule from human cells to bacteria. Initially we had planned to use another AHL. However, we decided not to use AHLs as signal molecules from human cells to bacteria since AHLs cannot be synthesized by human cells due to lack of their materials [2]. Thus, we had to explore if there is a potential signaling molecule produced by human cells. To this end, <span style="font-style: italic">E. coli</span> cells were interacted with the supernatant of the medium which human cells were cultured. Then transcriptome analysis was conducted to observe if there were any differences in the gene expression in <span style="font-style: italic">E. coli</span>.</p>
+     <p style="font-size: 16px; text-indent: 1em"> In our project, we worked on establishing an artificial cross-kingdom communication between human cells and bacteria. However, the cross-kingdom communication was not known well. Therefore,  we first had to choose appropriate signaling molecules to establish it. We chose one of the AHL molecules, 3OC8HSL, as a signaling molecule from bacteria to human cells. This is because it can interact with only genetically engineered human cells (Read <a href="https://2017.igem.org/Team:TokyoTech/Experiment/TraI_Assay">TraI Assay</a> page). Next, we had to choose a signaling molecule from human cells to bacteria. Initially we had planned to use another AHL. However, we decided not to use AHLs as signal molecules from human cells to bacteria since AHLs cannot be synthesized by human cells due to lack of their materials [2]. Thus, we had to explore if there is a potential signaling molecule produced by human cells. To this end, <span style="font-style: italic">E. coli</span> cells were interacted with the supernatant of the medium which human cells were cultured. Then transcriptome analysis was conducted to observe if there were any differences in the gene expression in <span style="font-style: italic">E. coli</span>.</p>
      </p>
@@ Line 132: / Line 154: @@
      <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Summary</b></h1><!-- 小見出し -->
      <hr style="width:50px;border:5px solid red" class="w3-round">
-    <p style="font-family: Poppins;font-size: 16px"><p style="text-indent:1em">We checked the difference of transcription between <span style="font-style: italic">E. coli</span> in normal medium and <span style="font-style: italic">E. coli</span> in the medium which human cells were cultured. Surprisingly, there were no significant differences in almost all of the RNA expressions except for  a couple of genes. The difference was only a little even for those genes. </p>
+        <p style="font-size: 16px; text-indent: 1em">We checked the difference of transcription between <span style="font-style: italic">E. coli</span> in normal medium and <span style="font-style: italic">E. coli</span> in the medium which human cells were cultured. Surprisingly, there were no significant differences in almost all of the RNA expressions except for  a couple of genes. The difference was only a little even for those genes. </p>
 <div style="margin-top:16px">
 <p style="text-indent:1em"> </p>
@@ Line 149: / Line 171: @@
-    <p style="font-family: Poppins;font-size: 16px"><p style="text-indent:1em">This excel file is the data of the transcriptome analysis. The value of E- FDR of the all genes was 1.<center><a href="https://2017.igem.org/File:T--TokyoTech--Transcriptome_Analysis.xlsx">The result data of transcription analysis</a>
+        <p style="font-size: 16px; text-indent: 1em">The 4318 genes were checked and <span style="font-style: italic">malG</span>coding Maltose transport system permease protein MalG and <span style="font-style: italic">malF</span>coding Maltose transport system permease protein MalF were transcribed about 1.7-fold. This excel file is the data of the transcriptome analysis. The value of E- FDR of the all genes was 1.<center><a href="https://2017.igem.org/File:T--TokyoTech--Transcriptome_Analysis.xlsx">Click here to download the result data</a>
      	</center>
 </p>
@@ Line 165: / Line 187: @@
      <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Discussion</b></h1>
      <hr style="width:50px;border:5px solid red" class="w3-round">
-     <p style="font-family: Poppins;font-size: 16px"><p style="text-indent:1em">It said that the difference is statistically significant if the value of E-FDR is 0.5 or less.  Therefore, the results show that most of the genes were not activated or repressed by substances derived from human cells. Two genes related to maltose metabolism were transcribed about 1.7-fold higher. This fact indicates that a substance like maltose is secreted from human cells. However, it is not proper for a signaling molecule because the activation rate is very low. Considering this result, no substances derived from human can be used as our ideal signaling molecule. Therefore, we have to explore another substance which works as a signaling molecule (Read <a href="https://2017.igem.org/Team:TokyoTech/AHK4">AHK4 Assay</a> page and Project page).
+     <p style="font-size: 16px; text-indent: 1em">It is said that the difference is statistically significant if the value of E-FDR is 0.5 or less.  Therefore, the results showed that most of the genes were not activated or repressed by substances derived from human cells. Two genes related to maltose metabolism were transcribed about 1.7-fold higher. This fact indicates that a substance like maltose was secreted from human cells. However, it was not proper for a signaling molecule because the activation rate was very low. Considering this result, no substances derived from human could be used as our ideal signaling molecule. Therefore, we had to explore another substance which works as a signaling molecule (Read <a href="https://2017.igem.org/Team:TokyoTech/Experiment/AHK4_Assay">AHK4 Assay</a> page and Project page).
@@ Line 172: / Line 194: @@
 </div>
+<hr>
+   <div id="mtt" class="w3-container" id="overview" style="margin-top:20px">
+    <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b> Appendix: Material and Method</b></h2>
+    <hr style="width:50px;border:5px solid red" class="w3-round">
+      <center>
+    <object data="https://static.igem.org/mediawiki/2017/a/aa/TraI_improve.pdf" type="application/pdf" style="width: 70%; height: 800px"></object>
+    </center>
+    </div>
 <hr>
@@ Line 178: / Line 210: @@
      <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Reference</b></h1>
      <hr style="width:50px;border:5px solid red" class="w3-round">
-     <p style="font-family: Poppins;font-size: 16px"><p style="text-indent:1em">[1] Foundational Platform for Mammalian Synthetic Biology, 2012 Noah Davidsohn et.al
+        <p style="font-size: 16px; text-indent: 1em">[1] Foundational Platform for Mammalian Synthetic Biology, 2012 Noah Davidsohn et.al
-     <p style="font-family: Poppins;font-size: 16px"><p style="text-indent:1em">[2] Multiple reference genomes and transcriptomes for <span style="font-style: italic">Arabidopsis thaliana</span>, 2011 Xiangchao Gan et.al
+        <p style="font-size: 16px; text-indent: 1em">[2] Multiple reference genomes and transcriptomes for <span style="font-style: italic">Arabidopsis thaliana</span>, 2011 Xiangchao Gan et.al
       </p>
       </p>
+</div>
-<div style="margin-top:16px">
-   </div>
+</div>
 </div><!-- ここまでが編集可能範囲 -->
-<div class="w3-light-grey w3-container w3-padding-32" style="margin-top:75px;padding-right:58px"><p class="w3-right">Hajime Fujita:  <a href="96haji.me" title="W3.CSS" target="_blank" class="w3-hover-opacity">All Rights Reserved</a></p></div>
+ <div class="w3-container" id="contact" style="margin-top:20px">
+ <p id="pageTop" style="text-align:right"><a href="#wrap"><img src="https://static.igem.org/mediawiki/2017/0/0d/T--TokyoTech--page_top_2.png" style="width:200px"></a></p>
+</div>
+<!-- W3.CSS Container -->
+<div class="w3-light-grey w3-container w3-padding-32" style="margin-top:75px;padding-right:58px"><p class="w3-right"><a href="http://96haji.me/" title="W3.CSS" target="_blank" class="w3-hover-opacity">Hajime Fujita with W3.CSS: All Rights Reserved</a></p></div>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>
 <script>
 // Script to open and close sidebar
@@ Line 201: / Line 238: @@
      document.getElementById("myOverlay").style.display = "none";
 }
+</script>
+<script>
 // Modal Image Gallery
 function onClick(element) {
@@ Line 209: / Line 247: @@
    captionText.innerHTML = element.alt;
 }
+$(function() {
+  var h = $(window).height();
+  $('#wrap').css('display','none');
+  $('#loader-bg ,#loader').height(h).css('display','block');
+});
+$(window).load(function () { //全ての読み込みが完了したら実行
+  $('#loader-bg').delay(900).fadeOut(800);
+  $('#loader').delay(600).fadeOut(300);
+  $('#wrap').css('display', 'block');
+});
 </script>
+<script>
+//■page topボタン
+$(function(){
+var topBtn=$('#pageTop');
+topBtn.hide();
+//◇ボタンの表示設定
+$(window).scroll(function(){
+  if($(this).scrollTop()>80){
+    //---- 画面を80pxスクロールしたら、ボタンを表示する
+    topBtn.fadeIn();
+  }else{
+    //---- 画面が80pxより上なら、ボタンを表示しない
+    topBtn.fadeOut();
+  }
+});
+// ◇ボタンをクリックしたら、スクロールして上に戻る
+topBtn.click(function(){
+  $('body,html').animate({
+  scrollTop: 0},500);
+  return false;
+});
+});
+</script>
 </body>
 </html>

Difference between revisions of "Team:TokyoTech/Experiment/Transcriptome Analysis"