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

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     <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Introduction</b></h1><!-- 小見出し -->
 
     <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">
 
     <hr style="width:50px;border:5px solid red" class="w3-round">
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    <p style="font-family: Poppins;font-size: 16px"><p style="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 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>
  
 
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     <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Summary</b></h1><!-- 小見出し -->
 
     <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">
 
     <hr style="width:50px;border:5px solid red" class="w3-round">
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    <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">
 
<div style="margin-top:16px">
 
<p style="text-indent:1em"> </p>
 
<p style="text-indent:1em"> </p>
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    <p style="font-family: Poppins;font-size: 16px"><p style="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>
+
        <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>
 
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</p>
 
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     <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Discussion</b></h1>
 
     <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Discussion</b></h1>
 
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     <hr style="width:50px;border:5px solid red" class="w3-round">
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     <p style="font-family: Poppins;font-size: 16px"><p style="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).
+
     <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).
  
  
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     <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Reference</b></h1>
 
     <h1 class="w3-xxxlarge w3-text-red" style="padding-bottom: 10px;padding-top: 10px"><b>Reference</b></h1>
 
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    <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
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        <p style="font-size: 16px; text-indent: 1em">[1] Foundational Platform for Mammalian Synthetic Biology, 2012 Noah Davidsohn et.al
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    <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
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        <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
 
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Revision as of 12:27, 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

Hajime Fujita: All Rights Reserved