Team:NJU China/Wet lab

From 2013.igem.org

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Line 59: Line 59:
     float:left;
     float:left;
     white-space: nowrap;
     white-space: nowrap;
-
     top:-3px;
+
     top:-6px;
     width: 490px;
     width: 490px;
     z-index: 5000;
     z-index: 5000;
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}
}
abbr,acronym { border:0;
abbr,acronym { border:0;
 +
}
 +
/* MAIN STYLE DEFINITIONS */
 +
a{
 +
color:#870203;
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-webkit-transition-duration:0.3s;
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-moz-transition-duration:0.3s;
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-o-transition-duration:0.3s;
}
}
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a:hover {
 +
color:#3d3f3c;
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}
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a:visited{
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color:#870203;
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}
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td
 +
{
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font-family: Helvetica;
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font-size: 10pt;
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vertical-align: top;
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text-align: left;
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padding-right: 10px;
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}
 +
 +
tr
 +
{
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vertical-align: top;
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}
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H1 {
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    font-family: Helvetica;
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 +
    color: #3d3f3c;
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    text-align: left;
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    }
 +
 +
 
 +
H4 {
 +
    font-family: Helvetica;
 +
 +
    color: #3d3f3c;
 +
    text-align: left;
 +
    }
 +
 +
/* CONTENT HEADING STYLES - overrides some main.css styling */
 +
 +
H6 {
 +
font-family:'Caviar Dreams';
 +
font-size:30px;
 +
font-weight:500;
 +
text-align:left;
 +
 +
color: #3d3f3c;
 +
border-bottom:1px solid orangered;
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padding-bottom:10px;
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margin:15px 0;
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}
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H1, H3 {
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font-family:'Tahoma';
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font-weight:100;
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}
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H1 {
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font-size:20px;
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border:none;
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}
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img.headshot {
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width: 100px;
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height: auto;
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vertical-align: text-top;
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}
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body {
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background:#fff;
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font-family: Helvetica;
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#tracking_nav
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{
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color:#bababa;
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background:#3d3f3c;
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font-size: 16pt;
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padding: 5px;
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line-height: 120%;
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#tracking_nav a { color:#ffffff;font-size: 16pt;}
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#tracking_nav a:hover {background:#bababa;}
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#parts_table
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{
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border: 1px solid #870203;
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width: 70%;
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margin: auto;
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}
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#parts_table td
 +
{
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text-align: center;
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margin: 5px;
 +
border: 1px solid #870203;
 +
 +
}
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 +
#parts_table th
 +
{
 +
background-color: #bababa;
 +
border: 1px solid #870203;
 +
color: #ffffff;
 +
}
 +
 +
.table_part
 +
{
 +
vertical-align: middle;
 +
}
 +
 +
/* HEADER STYLES: banner, navbar, etc. */
 +
#banner { width:300px; display:block; float:left; }
 +
#banner img { width:100%; }
 +
 +
ul#nav {
 +
width:1800px;
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margin:15px 0 0 400px;
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position:relative;
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}
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#nav li {
 +
color: #bbb;
 +
background-color:none;
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margin: 0 50px 0 0;
 +
float: left;
 +
position: relative;
 +
list-style: none;
 +
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}
 +
#nav li:last-child { margin:0; }
 +
 +
/* main level link */
 +
#nav a {
 +
font-family:'Source Sans Pro', sans-serif;
 +
font-size:10pt;
 +
font-weight:500;
 +
line-height:110%;
 +
color: inherit;
 +
text-decoration: none;
 +
display: block;
 +
padding: 0 0 0 5px;
 +
margin: 0;
 +
}
 +
 +
ul#nav > li > a {
 +
line-height:12px;
 +
border-left:solid 2px #bbb;
 +
padding:0 0 0 3px;
 +
}
 +
 +
#nav a:hover {
 +
/*background-color: #870203;
 +
color: #ffffff;*/
 +
}
 +
 +
/* main level link hover */
 +
#nav .current a, #nav li:hover > a {
 +
color: #000;
 +
border-color:orangered;
 +
}
 +
 +
/* sub levels link hover */
 +
#nav ul li:hover a, #nav li:hover li a {
 +
border: none;
 +
/*background-color: #FA9D1C;*/
 +
color:#000;
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}
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#nav ul a:hover {
 +
color: orangered !important;
 +
/*background: #fff url(img/gradient.png) repeat-x 0 -100px !important;
 +
text-shadow: 0 1px 1px rgba(0,0,0, .1);*/
 +
}
 +
 +
 +
/* dropdown */
 +
#nav li:hover > ul {
 +
/*display: block;*/
 +
opacity:1;
 +
margin:0;
 +
background-color: none;
 +
z-index:0;
 +
}
 +
 +
/* level 2 list */
 +
#nav ul {
 +
/*display: none;*/
 +
opacity:0;
 +
margin: 20px 0 0 0;
 +
padding: 7px 0 0 0;
 +
width: 205px;
 +
position: absolute;
 +
left: 0;
 +
z-index:-1;
 +
-webkit-transition-duration:0.5s;
 +
-moz-transition-duration:0.5s;
 +
-o-transition-duration:0.5s;
 +
}
 +
#nav ul li {
 +
float: none;
 +
margin: 0;
 +
padding: 0;
 +
}
 +
 +
#nav ul a {
 +
font-weight: normal;
 +
/*text-shadow: 0 1px 0 #fff;*/
 +
}
 +
 +
/* clearfix */
 +
#nav:after {
 +
content: ".";
 +
display: block;
 +
clear: both;
 +
visibility: hidden;
 +
line-height: 0;
 +
height: 0;
 +
}
 +
#nav {
 +
display: inline-block;
 +
}
 +
html[xmlns] #nav {
 +
display: block;
 +
}
 +
 +
* html #nav {
 +
height: 1%;
 +
}
 +
 +
/* pinterest like photo grid for social page*/
 +
 +
/*
 +
body {
 +
background: url(http://subtlepatterns.com/patterns/scribble_light.png) ;
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}
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*/
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#wrapper {
 +
width: 90%;
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max-width: 1100px;
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min-width: 800px;
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margin: 50px auto;
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}
 +
 +
#columns {
 +
-webkit-column-count: 3;
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-webkit-column-gap: 10px;
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-webkit-column-fill: auto;
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-moz-column-count: 3;
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-moz-column-gap: 10px;
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-moz-column-fill: auto;
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column-count: 3;
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column-gap: 15px;
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column-fill: auto;
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.pin {
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display: inline-block;
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background: #FEFEFE;
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border: 2px solid #FAFAFA;
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box-shadow: 0 1px 2px rgba(34, 25, 25, 0.4);
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margin: 0 2px 15px;
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-webkit-column-break-inside: avoid;
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-moz-column-break-inside: avoid;
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column-break-inside: avoid;
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padding: 15px;
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padding-bottom: 5px;
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background: -webkit-linear-gradient(45deg, #FFF, #F9F9F9);
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opacity: 1;
 +
 +
-webkit-transition: all .2s ease;
 +
-moz-transition: all .2s ease;
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-o-transition: all .2s ease;
 +
transition: all .2s ease;
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}
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.pin img {
 +
width: 100%;
 +
border-bottom: 1px solid #ccc;
 +
padding-bottom: 15px;
 +
margin-bottom: 5px;
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 +
 +
.pin p {
 +
font: 12px/18px Arial, sans-serif;
 +
color: #333;
 +
margin: 0;
 +
}
 +
 +
@media (min-width: 960px) {
 +
#columns {
 +
-webkit-column-count: 4;
 +
-moz-column-count: 4;
 +
column-count: 4;
 +
}
 +
}
 +
 +
@media (min-width: 1100px) {
 +
#columns {
 +
-webkit-column-count: 5;
 +
-moz-column-count: 5;
 +
column-count: 5;
 +
}
 +
}
 +
 +
#columns:hover .pin:not(:hover) {
 +
opacity: 0.4;
 +
}
/* General Demo Style */
/* General Demo Style */
body{
body{
Line 273: Line 600:
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     text-transform: uppercase;
     color: rgba(0,0,0,0.8);
     color: rgba(0,0,0,0.8);
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text-shadow: 1px 1px 2px rgba(0,0,0,0.2);
text-shadow: 1px 1px 2px rgba(0,0,0,0.2);
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h2.ss-subtitle:before{
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h2.ss-subtitle:after{
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.ss-links{
.ss-links{
position: fixed;
position: fixed;
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     padding-right: 2%;
     padding-right: 2%;
}
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-
.ss-circle{
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background-color: #f0f0f0;
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.ss-small .ss-circle{
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.ss-medium .ss-circle{
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.ss-circle-deco:before{
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width: 29%;
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border-bottom: 5px dotted #ddd;
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border-bottom: 5px dotted rgba(17, 17, 22, 0.3);
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-webkit-box-shadow: 0px 1px 1px #fff;
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-moz-box-shadow: 0px 1px 1px #fff;
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-
box-shadow: 0px 1px 1px #fff;
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position: absolute;
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top: 50%;
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content: '';
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margin-top: -3px;
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.ss-circle-deco:after{
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border-top: 10px solid transparent;
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    border-bottom: 10px solid transparent;
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content: '';
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position: absolute;
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top: 50%;
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margin-top: -10px;
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.ss-left .ss-circle-deco:before{
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    right: 2%; 
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.ss-right .ss-circle-deco:before{
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border-left: 10px solid rgba(17,17,22,0.8);
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    float: right;
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    margin-right: 30%;
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.ss-container h3{
     margin-top: 34px;
     margin-top: 34px;
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</script>
</script>
-
</head>
+
    </head>
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<body>
+
    <body>
 +
<div style="float:left; position:absolute; margin-top:-15px; margin-left:325px; z-index:1; display:block; ">
 +
</br></br>
 +
<a href="https://2013.igem.org"><img src="https://static.igem.org/mediawiki/2013/8/80/NJU-Miniminiminilogocolored.png" ></a>
 +
</div>
         <p>&nbsp;</p>
         <p>&nbsp;</p>
         <div class="container">
         <div class="container">
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         <ul>  
         <ul>  
  <li><a href="http://https://2013.igem.org/Team:NJU_China/Project#Overview">Overview</a></li>  
  <li><a href="http://https://2013.igem.org/Team:NJU_China/Project#Overview">Overview</a></li>  
-
           <li><a https://2013.igem.org/Team:NJU_China/Project#Chassis">Chassis</a></li>  
+
           <li><a href="https://2013.igem.org/Team:NJU_China/Project#Chassis">Chassis</a></li>  
-
           <li><a https://2013.igem.org/Team:NJU_China/Project#Targeting Module">Targeting Module</a></li>  
+
           <li><a href="https://2013.igem.org/Team:NJU_China/Project#Targeting Module">Targeting Module</a></li>  
-
           <li><a https://2013.igem.org/Team:NJU_China/Project#Killing Module">Killing Module</a></li>  
+
           <li><a href="https://2013.igem.org/Team:NJU_China/Project#Killing Module">Killing Module</a></li>  
-
           <li><a https://2013.igem.org/Team:NJU_China/Project#Achievement">Achievement</a></li>
+
           <li><a href="https://2013.igem.org/Team:NJU_China/Project#Achievement">Achievement</a></li>
         </ul>
         </ul>
     </li>
     </li>
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         <ul>  
         <ul>  
  <li><a href="http://https://2013.igem.org/Team:NJU_China/Project#Free debate">Free debate</a></li>  
  <li><a href="http://https://2013.igem.org/Team:NJU_China/Project#Free debate">Free debate</a></li>  
-
           <li><a https://2013.igem.org/Team:NJU_China/Project#Reach the unreached">Reach the unreached</a></li>  
+
           <li><a href="https://2013.igem.org/Team:NJU_China/Project#Reach the unreached">Reach the unreached</a></li>  
-
           <li><a https://2013.igem.org/Team:NJU_China/Project#Workshop">Workshop</a></li>  
+
           <li><a href="https://2013.igem.org/Team:NJU_China/Project#Workshop">Workshop</a></li>  
-
           <li><a https://2013.igem.org/Team:NJU_China/Project#Collaboration">Collaboration</a></li>  
+
           <li><a href="https://2013.igem.org/Team:NJU_China/Project#Collaboration">Collaboration</a></li>  
         </ul>
         </ul>
     </li>
     </li>
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         <ul>  
         <ul>  
  <li><a href="http://https://2013.igem.org/Team:NJU_China/Project#Protocol">Protocol</a></li>  
  <li><a href="http://https://2013.igem.org/Team:NJU_China/Project#Protocol">Protocol</a></li>  
-
           <li><a https://2013.igem.org/Team:NJU_China/Project#Reach the unreached">Lab notes</a></li>  
+
           <li><a href="https://2013.igem.org/Team:NJU_China/Notebook">Lab notes</a></li>  
-
           <li><a https://2013.igem.org/Team:NJU_China/Project#Workshop">Data Page</a></li>  
+
           <li><a href="https://2013.igem.org/Team:NJU_China/Data_Page">Data Page</a></li>  
-
           <li><a https://2013.igem.org/Team:NJU_China/Project#Collaboration">Parts</a></li>  
+
           <li><a href="https://2013.igem.org/Team:NJU_China/Parts">Parts</a></li>  
         </ul>
         </ul>
     </li>  
     </li>  
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     <li><a href="https://2013.igem.org/Team:NJU_China/Safety">Safety</a>
     <li><a href="https://2013.igem.org/Team:NJU_China/Safety">Safety</a>
         <ul>  
         <ul>  
-
  <li><a href="http://https://2013.igem.org/Team:NJU_China/Project#Protocol">Safety form</a></li>  
+
  <li><a href="https://2013.igem.org/Team:NJU_China/Safety">Safety form</a></li>  
-
           <li><a https://2013.igem.org/Team:NJU_China/Project#Reach the unreached">Virus-related safety</a></li>  
+
           <li><a href="https://2013.igem.org/Team:NJU_China/Virus-related_safety">Virus-related safety</a></li>  
         </ul>
         </ul>
     </li>  
     </li>  
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     <li><a href="https://2013.igem.org/Team:NJU_China/Extras">Extras</a>
     <li><a href="https://2013.igem.org/Team:NJU_China/Extras">Extras</a>
             <ul>  
             <ul>  
-
  <li><a href="http://https://2013.igem.org/Team:NJU_China/Project#Protocol">Judging criteria</a></li>  
+
  <li><a href="https://igem.org/2013_Judging_Form?id=1180">Judging criteria</a></li>  
-
           <li><a https://2013.igem.org/Team:NJU_China/Project#Reach the unreached">Attribution</a></li>  
+
           <li><a href="https://2013.igem.org/Team:NJU_China/Extras">Attribution</a></li>  
-
           <li><a https://2013.igem.org/Team:NJU_China/Project#Reach the unreached">Acknowledgement</a></li>
+
           <li><a href="https://2013.igem.org/Team:NJU_China/Acknowledgement">Acknowledgement</a></li>
         </ul>
         </ul>
     </li>
     </li>
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</ul>
</ul>
-
<!--End NavBar-->
+
<!--End NavBar-->  
-
             <h2 class="ss-subtitle">Notebook</h2>
+
             <h2 class="ss-subtitle">Notebook</h2>  
<div id="ss-links" class="ss-links">
<div id="ss-links" class="ss-links">
<a href="#March">Mar</a>
<a href="#March">Mar</a>
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<a href="#August">Aug</a>
<a href="#August">Aug</a>
                                 <a href="#September">Sep</a>
                                 <a href="#September">Sep</a>
 +
                                <a href="#October">Oct</a>
</div>
</div>
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<h3>
<h3>
<a>WEEK 8</a>
<a>WEEK 8</a>
-
<span>5th-15th, July</span>
+
<span>19th-24th, June</span>
 +
</h3>
 +
</div>
 +
<div class="ss-right">
 +
<h3>
 +
<a>siRNA screening (failed)</a>
 +
<span>
 +
8th: We cultured Hep G2 cells in 2 12-well plates for 24-hour cell collection and 48-hour cell collection.</br>
 +
9th: We transfected cells with empty Lipo, HbsAg plasmids, HbsAg plasmids and 467 siRNA plasmids, HbsAg plasmids and 516 siRNA plasmids, respectively.</br>
 +
10th: We collected cells 24 hours after transfection, and preserved them in Trizol.</br>
 +
11th: We collected 48 hours after transfection, and then extracted RNA from 2 groups of cells (24 hours and 48 hours).</br>
 +
12th: We did RT-PCR and qPCR with all RNA samples.</br>
 +
13th: We analyzed the data.</br>
 +
</span>                           
 +
</h3>
 +
</div>
 +
</div>
 +
 
 +
            <div class="ss-row">
 +
                    <div class="ss-left">
 +
                    <h2 id="July">July</h2>
 +
                    </div>
 +
                    <div class="ss-right">
 +
                    <h2>2013</h2>
 +
                    </div>
 +
                    </div>
 +
 
 +
<div class="ss-row ss-medium">
 +
<div class="ss-left">
 +
<h3>
 +
<a>WEEK 8</a>
 +
<span>19th-24th, June</span>
</h3>
</h3>
</div>
</div>
Line 843: Line 1,107:
26th: We analyzed data and found that the standard curve cannot be used.</br>
26th: We analyzed data and found that the standard curve cannot be used.</br>
27th: We redid the Q-PCR and analyzed data and this time we succeeded</br>
27th: We redid the Q-PCR and analyzed data and this time we succeeded</br>
-
</span> 
 
-
<a>Luciferase Assay</a>
 
-
<span>
 
-
16th: We digested single plasmid and separated the vector segments and insert segments by agarose gel electrophoresis.</br>
 
-
17th: We recycled the vector segments from agarose gel we used in 16th July.</br>
 
-
18th: We synthesized 467 and 516 double-strand DNA segments from the primer of 467 and 516 RNA. Then we linked these two kinds of DNA segments with the vector segments we got in 17th July respectively overnight at 16℃ to get recombinant plasmids.</br>
 
-
19th: We transformed the 467/516 recombinant plasmids we got in 18th July into E.coli DH5α Competent Cells respectively and spread these cells on the surface of solid LB medium added ampicillin.</br>
 
-
20th: We transferred 4 single colonies both of 467/516 recombinant plasmids containing E.coli into fluid LB culture medium with ampicillin, and shaken the medium overnight at 37℃.</br>
 
-
21th: We preserved 467/516 strains at -80℃ and sent 1mL of each culture medium to sequencing firm for sequencing. Then we extracted plasmids from the rest culture medium shaken in 20th July.</br>
 
-
22th: We digested the 467/516 recombinant plasmids we extracted in 21th July respectively and tested the results of recombination by agarose gel electrophoresis.</br>
 
-
25th: We received sequencing results from sequencing firm, and after comparing them with the results of agarose gel electrophoresis, we confirmed that we constructed the 467/516 recombinatiant plasmids successfully and got relevant E.coli strains.</br>
 
</span>   
</span>   
<a>Examination whether RVG-lamp2b exosomes will target to dendritic cells or not (failed)</a>
<a>Examination whether RVG-lamp2b exosomes will target to dendritic cells or not (failed)</a>
Line 1,058: Line 1,311:
<h3>
<h3>
<a>WEEK 16-17</a>
<a>WEEK 16-17</a>
-
<span>2th-14th, September</span>
+
<span>2th-11th, September</span>
</h3>
</h3>
</div>
</div>
Line 1,071: Line 1,324:
4th: We redid RT-PCR and Q-PCR on 3th September.</br>
4th: We redid RT-PCR and Q-PCR on 3th September.</br>
</span>                             
</span>                             
-
<a>Collection of Exosomes containing 467 plasmids</a>
+
<a>Exosomes collection</a>
<span>
<span>
-
2th: We subclutured five 225 cm2 flasks of 293T cells.</br>
 
4th: We transfected 293T cells with 467 plasmids.</br>
4th: We transfected 293T cells with 467 plasmids.</br>
5th: We soaked centrifuge tubes which then be used in ultracentrifugation overnight in DEPC solution(1:1000).</br>
5th: We soaked centrifuge tubes which then be used in ultracentrifugation overnight in DEPC solution(1:1000).</br>
6th: We collected culture medium and separated exosomes by ultracentrifugation and stored the exosome solution at 4℃.</br>
6th: We collected culture medium and separated exosomes by ultracentrifugation and stored the exosome solution at 4℃.</br>
-
8th: We examined protein concentration of exosomes collected on 6th September.</br>
 
-
</span>                           
 
-
<a>Collection of Empty Exosomes</a>
 
-
<span>
 
-
9th: We subclutured five 225 cm2 flasks of 293T cells.</br>
 
-
11th: We transfected 293T cells with nothing and changed culture media after 6 hours.</br>
 
-
12th: We soaked centrifuge tubes which then be used in ultracentrifugation overnight in DEPC solution(1:1000).</br>
 
-
14th: We collected culture medium and separated exosomes by ultracentrifugation and examined protein concentration of exosomes. Stored the exosomes solution at 4℃.</br>
 
</span>   
</span>   
<a>Construction of standardized plasmid</a>
<a>Construction of standardized plasmid</a>
Line 1,100: Line 1,344:
11th: We got result of sequencing from GenScript. We constructed standardized 467-plasmid successfully.</br>
11th: We got result of sequencing from GenScript. We constructed standardized 467-plasmid successfully.</br>
</span>   
</span>   
-
<a>Others:</a>
 
-
<span>
 
-
13th: We subcultured eight 225cm2 falsks of 293T cells.</br>
 
-
<span>
 
</h3>
</h3>
</div>
</div>
</div>
</div>
 +
 +
            <div class="ss-row">
 +
                    <div class="ss-left">
 +
                    <h2 id="October">October</h2>
 +
                    </div>
 +
                    <div class="ss-right">
 +
                    <h2>2013</h2>
 +
                    </div>
 +
                    </div>
<div class="ss-row ss-medium">
<div class="ss-row ss-medium">
<div class="ss-left">
<div class="ss-left">
<h3>
<h3>
-
<a>WEEK 18-19</a>
+
<a>Week 1</a>
-
<span>15th-25th, September</span>
+
<span>12th-19th, October</span>
</h3>
</h3>
</div>
</div>
<div class="ss-right">
<div class="ss-right">
<h3>
<h3>
-
<a>Pre-S1 Liver-targeting experiment</a>
 
-
<span>
 
-
16th: We subcultured four 225cm2 falsks of 293T cells.</br>
 
-
18th: We subcultured sixteen 225cm2 falsks of 293T cells.</br>
 
-
20th: We transfected fifteen 225cm2 falsks of 293T cells with plasmids (empty*5, 467*5, pre-s1+467*5).</br>
 
-
21th: We soaked centrifuge tubes which then be used in ultracentrifugation overnight in DEPC solution(1:1000).</br>
 
-
22th: We collected culture medium and separated exosomes by ultracentrifugation, examined protein concentration and extracted RNA from 30 μL exosome solution and stored the rest exosome solution at 4℃.</br>
 
-
23th: We did RT-PCR and q-PCR with the RNA we extracted on 22th for absolute quantification. We dosed mice with exosomes (empty, 467, pre-s1+467) by tail intravenous injection.</br>
 
-
24th: We anatomized C57 HBsAg model mice and collected the heart, liver, spleen, lung, kidney and blood of them and preserved these tissues at -80℃. We centrifuged blood at 1000*g for 10 min and preserved serum at -80℃. Then we extracted RNA from liver, lung and serum we collected today and examined RNA concentration.</br>
 
-
25th: We did RT-PCR and q-PCR with the RNA we extracted on 24th and analyzed data.</br>
 
<span>
<span>
 +
12th : Subcultured 293T cells to six 225 cm2  flasks and three 75 cm2  flasks .</br>
 +
14th：Transferred 293T cells with plasmids and microRNA.For the six 225cm2  flasks , three groups : lipo*2, mirco162 RNA*2, micro162 RNA + GP120 plasmid(targeting to T cell) *26 hours After transfecting, Changed the culture mediaSubcultured 293T cells.</br>
 +
15th : Soaked centrifuge tubes which will be used in ultracentrifugation over night in ddH2O</br>
 +
16th: Collected 36-hour~48-hour culture containing exosomes.(The cells transfected with micro162 were contaminated by bacterium). Did pre-centrifuge(1500g:10min; 10000g: 30min). Separated exosomes by ultracentrifugation. Examine protein concentration of exosomes.Subcultured 293T cells.</br>
 +
17th: Separated T cells from the spleen of mouse, cultured the cells in 24-well plate, Each well contained 10^5 cells. cocultured empty exosomes and mirco162+GP120 exosomes with T cell respectively, each well added 10ug exosomes.Cultured HepG2 cells to 15 wells in 96-well plate, and did 4 plates. </br>
 +
18th : collected T cell in 12-well plate, separated CD4+ cells and CD4- cells using CD4+ T cell isolation Kit ,and started to extract RNA from the cells respectively, and then RT-Q-PCR.Subcultured 293T cells.HepG2 cells were contaminated by bacterium.</br>
 +
19th :  Analyzed data.</br>
 +
</span>                           
</h3>
</h3>
</div>
</div>
Line 1,134: Line 1,381:
 +
<div class="ss-row ss-medium">
 +
<div class="ss-left">
 +
<h3>
 +
<a>Week 2</a>
 +
<span>20th-26th, October</span>
 +
</h3>
 +
</div>
 +
<div class="ss-right">
 +
<h3>
 +
<span>
 +
20th :  Subcultured 293T cells</br>
 +
22th : transferred 293T cells with plasmids and microRNA(before transfecting, collected the medium for empty exosomes).For twelve 225 cm2  flasks, micro162 RNA*2, micro162 RNA+ GP120 plasmid *2, GFP inhibit siRNA *8;  For  twenty four 75 cm2  flasks, GFP inhibit siRNA + pres1 plasmid;cultured HepG2 cells to 15 wells in 96-well plate, and did 5 plates.</br>
 +
23th : Separated T cells from the spleen of mouse, cultured the cells in 24-well plate, Each well contained 3.2 *10^5 cells. (0 hours after adding exosomes into HepG2 cells) collected the medium of one plate with HepG2 cells for elisa. And Added 10ul CCK reagent and put the plate in incubator for 3hours, then tested it’s OD value. Add exosomes into HepG2 cells in each plate of the remaining four: PBS 10ul each well *5; empty exosomes 10ul(3ug) each well *5; micro162+GP120 exosomes 10ul(3ug) each well *5; Soaked centrifuge tubes which will be used in ultracentrifugation over night in ddH2O</br>
 +
24th : Collected 36-hour~48-hour culture containing exosomes.Cocultured empty exosomes, mirco162 exosomes and mirco162+GP120 exosomes  with T cell respectively, each well added 10ug exosomes.12 hours after adding exosomes into HepG2 cells, collected the medium for elisa. Added 10ul CCK reagent and put the plate in incubator for 3hours, then tested it’s OD value. For 24/36/48 hours after adding exosomes into HepG2 cells, did the same experiments as 0/12hours.</br>
 +
25th : Collected T cell in 12-well plate, separated CD4+ cells and CD4- cells using CD4+ T cell isolation Kit ,and started to extract RNA from the cells respectively, and then RT-Q-PCR.Got the OD value of 0/12/24/36/48 hours after adding exosomes in HepG2 cells. Injected three GFP mice with empty exosomes , exosomes containing GFP inhibit siRNA, and pres1-exosomes with GFP inhibit siRNA respectively twice. For the first time at 9 am and the second time at 9 pm.</br>
 +
26th : Analyzed data </br>
 +
Killed the three GFP mice and took out their liver respectively at 9 am. </br>
 +
Did a frozen section of the hepatic tissue.</br>
 +
Observed the slice of the tissue with the fluorescence microscope and took pictures.</br>
 +
Using the Human IL-6 Elisa kit, Human IL-8 Elisa kit and Human TNF-α Elisa kit to test OD450 value of the medium we collected 0/12/24/36/48 hours after adding exosomes in HepG2 cells. </br>
 +
Analyzed data.</br>
 +
</span> 
 +
</h3>
</div>
</div>
</div>
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Latest revision as of 01:22, 29 October 2013



 

Notebook

March

2013

WEEK 1 25th-28th, March

Experiment training We learnt to culture the 293t cells.
We learnt to extract plasmids and transfect it into 293t cells.
We learnt to collect exosomes.
We learnt to extract RNA from exosomes and cells.
We learnt to do RT-PCR and qPCR.

April

2013

WEEK 2 14th-18th, April

siRNA screening (Failed) 14th: We extracted plasmids and cultured the 293t cells.
15th: We transfected plasmids into 293t cells.
16th: We collected cells and preserved it in Trizol.
17th: We extracted RNA, then did RT-PCR with the RNA.
18th: We did qPCR with the cDNA we got on 17th April.
21th: We reexamined the concentration of RNA, and redid qPCR.

WEEK 3 27th, April – 1st, May

siRNA screening (Failed) 27th: We cultured the 293t cells in a 12-well plate.
28th: We transfected 293t cells.
29th: We collected cells and extracted RNA from it.
30th: We did RT-qPCR with the RNA we extracted on 29th April.
1st: We did qPCR with the cDNA we got on 30th April.

May

2013

WEEK 4 8th-13th, May

siRNA screening (Failed), examination whether siRNA are capsulated into exosomes (Success) 8th: We extracted plasmids of 3 kinds of siRNA.
9th: We cultured 293t cells in eight D10 dishes and a 12-well plate.
10th: We extracted 2 kinds of over-expression plasmids and examined the concentration of it. Then we transfect these plasmids into 293t cells respectively.
11th: We collected cells and exosomes from 8 D10 dish, and cells from 12-well plate.
12th: We extracted RNA from cells and exosomes.
13th: We did RT-PCR and qPCR.

WEEK 5 15th-18th, May

siRNA screening (Failed) 15th: We cultured the 293t cells in a 12-well plate.
16th: We transfected 293t cells.
17th: We collected cells and extracted RNA from then.
18th: We did RT-PCR and qPCR.

WEEK 6 27th-31th, May

siRNA screening (Failed) 27th: We cultured the 293t cells in 2 12-well plates.
28th: We transfected 293t cells, with lipofectamine 2000.
29th: We collected cells and extracted RNA from them.
30th: We continued to extract RNA, and examine the concentration of total RNA. Then we did RT-PCR.
31st : We did qPCR.

June

2013

WEEK 7 19th-24th, June

siRNA screening (eliminated 308 siRNA, 467 siRNA and 516 siRNA seem to have good effect) 19th: We cultured 293t cells in 12-well plates.
20th: We transfected 293t cells.
21st: We collected cells and preserved in Trizol.
22nd: We extracted RNA from cells and did RT-PCR.
24th: We did qPCR.

July

2013

WEEK 8 19th-24th, June

siRNA screening (failed) 8th: We cultured Hep G2 cells in 2 12-well plates for 24-hour cell collection and 48-hour cell collection.
9th: We transfected cells with empty Lipo, HbsAg plasmids, HbsAg plasmids and 467 siRNA plasmids, HbsAg plasmids and 516 siRNA plasmids, respectively.
10th: We collected cells 24 hours after transfection, and preserved them in Trizol.
11th: We collected 48 hours after transfection, and then extracted RNA from 2 groups of cells (24 hours and 48 hours).
12th: We did RT-PCR and qPCR with all RNA samples.
13th: We analyzed the data.

July

2013

WEEK 8 19th-24th, June

siRNA screening (failed) 8th: We cultured Hep G2 cells in 2 12-well plates for 24-hour cell collection and 48-hour cell collection.
9th: We transfected cells with empty Lipo, HbsAg plasmids, HbsAg plasmids and 467 siRNA plasmids, HbsAg plasmids and 516 siRNA plasmids, respectively.
10th: We collected cells 24 hours after transfection, and preserved them in Trizol.
11th: We collected 48 hours after transfection, and then extracted RNA from 2 groups of cells (24 hours and 48 hours).
12th: We did RT-PCR and qPCR with all RNA samples.
13th: We analyzed the data.
 Absolute quantification of exosomes (failed) 5th: We cultured 293t cells.
6th: Cells we cultured on 5th July were contaminated by bacteria.
7th: We subcultured another cell line of 293t cells.
9th: We cultured 293t cells in 6 flasks.
10th:We transferred 293T cells with plasmids.
11th: We collected exosomes 24 hours after transfection.
12th: A part of cells died, failed to collect 48-hour exosomes.
13th: We examined protein concentration of 24-hour exosomes, started to extract RNA from 24h-cells and 24h-exosomes and preserved the rough RNA extract solution with isopropyl alcohol at 4℃ overnight.
14th：We continued finish RNA extraction, then did RT-PCR and qPCR.
15th: We analyzed data.
 Luciferase Assay 11th: Construction of plasmids: obtain vector and segment.
12th: We combined vector and segment with T4 ligase, then transformed the recombined plasmids into E.coli DH5α competent cells and spread them on solid LB culture plates by streak plate method.
13th: No single bacterial colony was found.
14th: No single bacterial colony was found again, redid previous steps(obtain the target segments, combined vector and segment, and then transferred it into E.coli )
15th: Single bacterial colonies were found. We picked single colonies and transferred them into liquid LB culture medium with ampicillin, and shaken overnight at 37℃.
16th: The transformed E.coli cells failed to reproduce in LB culture medium.
 Others 5th: We thawed 293t cells.
6th: We subcultured HepG2 cells.
7th: E.coli cells containing HBSag overexpressed plasmids were transferred respectively into LB culture medium with ampicillin, and shaken overnight at 37℃.
8th: We extracted HBSag overexpressed plasmids from E.coli cells.
11th: We thawed 293t cells and subcultured HepG2 cells. E.coli cells containing GFP plasmids were transferred into LB culture medium with ampicillin, and shaken overnight at 37℃.
12th: We extracted GFP plasmids from E.coli cells.
14th: We thawed HepG2 cells and 293T cells.
15th: We thawed 293T cells.

WEEK 9 AND WEEK 10 16th -21th,22th-28th,July

Others 16th: We subcultured 293T cells. E.coli DH5α competent cells containing GFP plasmids and RVG plasmids were transferred respectively into LB culture medium with ampicillin, and shaken overnight at 37℃.
17th: We found that wrong antibiotics were added into the culture medium of RVG plasmid-containing E.coli cells (it ought to be kanamycin). So we did transferred E.coli cells containing RVG plasmids into LB culture medium with kanamycin), and shaken overnight at 37℃.
18th: We preserved the RVG and GFP strains at -80℃ and extracted plasmids from the culture medium (RVG,GFP, 1L medium). And cryopreserved 293T cells.
 Absolute quantification of exosomes (succeeded) 18th: We cultured 293t cells.
19th: We transfected 293T cells with 467 and 516 plasmids(lipo*2,467*2,516*2).
20th: We changed the transfection medium with culture medium and then collected culture medium containing exosomes 24 hours after transection (pre-centrifuge).
21th: We collected culture medium containing exosomes 48 hours after transfection (pre-centrifuge) and soaked.
centrifuge tubes which then be used in ultracentrifugation overnight in DEPC solution(1:1000).
22th: We separated exosomes by ultracentrifugation(110000g).
23th: We examined protein concentration of exosomes collected by ultracentrifugation, and then extracted RNA from these exosomes and cells which we used to produce exosomes and preserved the RNA extracts in isopropyl alcohol over night.
24th：We continued to extract RNA, examined total RNA concentration of exosomes and cells, then RT-PCR RNA 467 and 516.
25th: Q-PCR the cDNA of RNA 467 and 516.
26th: We analyzed data and found that the standard curve cannot be used.
27th: We redid the Q-PCR and analyzed data and this time we succeeded
 Examination whether RVG-lamp2b exosomes will target to dendritic cells or not (failed) 18th: We cultured 293t cells.
19th: We transfected 9 flasks of 293T cells with RVG plasmids(lipo*3,RVG*3,non-related plasmids*3).
20th: We changed the 19th transfection medium with cell culture medium 6 hours after transfection and transfected another 9 flasks of 293T cells as we did with the former 9 flasks.
21th: We collected 48-hour cell culture medium transfected on 19th July and pre-centrifuged to remove cell debris and organelles. We soaked centrifuge tubes which then be used in ultracentrifugation overnight in DEPC solution(1:1000).
22th: We collected 48-hour culture transfected on 20th July and pre-centrifuged to remove cell debris and organelles. Meanwhile, we watched green fluorescent in cells. Then we separated exosomes by ultracentrifugation (110000g).
23th: We examined protein concentration of exosomes collected on 22th July, diluted exosome solution from 500μL to 1000μL and filtered the exosome solution then injected exosome solution into the C57 mice. We took 3μL exosomes solution to extract RNA, and preserved RNA extracts in isopropyl alcohol over night.
24th：We continued to extract RNA, and examined total RNA concentration of exosomes and cells which we used to produce these exosomes, then RT –PCR.
25th: We injected exosome solution into the mice for the second time. Q-PCR the cDNA got from RT-PCR on 24th July.
26th: We analyzed data and found the standard curve cannot be used.
27th: We anatomized C57 mice and collected the brain, heart, liver, spleen, lung, kidney and blood of them and redid RT-PCR and Q-PCR with the RNA extracted on 24th July and analyzed data.
28th: We extracted RNA from brain and serum collected on 27th July

August

2013

WEEK 11 29th July-4th, August

Luciferase Assay (failed) 28th: We transfected 293T cells with plasmids in 24-well format.
29th: We did luciferase assay with 293T cells transfected on 28th July.
3th: We redid luciferase assay.
 Collection of exosomes containing 467 siRNA & 516 siRNA 29th: We transfected 4 flasks of 293T cells with 467 and 516 plasmids (467 plasmid*2, 516 plasmid*2).
31th: We collected 48-hour cell culture medium and pre-centrifuged it to remove cell debris and organelles and stored the medium at 4℃. We soaked centrifuge tubes which then be used in ultracentrifugation overnight in DEPC solution(1:1000).
1th: We separated exosomes by ultracentrifugation and stored the exosome solution at 4℃.
 Pre-experiment to examine whether anti 214 RNA is high in brain or not (failed) 30th: E.coli DH5α Competent Cells containing anti 214 plasmids were transferred into LB culture medium with spectinomycin, and shaken overnight at 37℃.
31th: We extracted anti 214 plasmid, subcultured 293T cells and transfected 293T cells with anti-214 plasmid. 1th: We collected 24-hour cells and preserved it in Trizol.
2th: We extracted RNA, RT-qPCR anti 214 RNA.
3th: We did agarose gel electrophoresis. Redid this pre-experiment.
 Others: 1th: We subcultured and cryopreserved 293T cells.
3th: E.coli DH5α Competent Cells transformed HER2 plasmids were transferred into LB culture medium with spectinomycin, and shaken overnight at 37℃.
4th: We extracted HER2 plasmids and examined DNA concentration.

WEEK 12 5th-12th, August

Pre-experiment to examine whether the expression level of anti 214/her2/467/516 RNA is high in brain or not (success) 7th: We subcultured 293T cells in 12-well format and transfected 293T cells with anti 214/her2/467/516 plasmids and changed the cell culture medium 6 hours after transfection.
8th: We extracted RNA from cells. RNA stored in -80℃.
10th: RT-PCR.
11th: Q-PCR and analyzed data.
12th: Redid the Q-PCR and analyzed data.
Coculture of HepG2 cells transformed HBsAg plasmids with exosomes containing 467 plasmid (failed) 7th: We subcultured HepG2 cells in 12-well format.
8th: We transfected HepG2 cells with HBsAg plasmids and added 467 exosomes into culture medium after 18 hours.
10th: We extracted RNA from HepG2 cells cocultured on 8th August and RT-PCR the RNA of HBsAg.
11th: We Q-PCR the cDNA we got on 10th August and analyzed data.
12th: We redid the Q-PCR and analyzed data.
 Others: 7th: We examines protein concentration of exosomes (467, 516 and empty)

WEEK 13 12th-18th, August

Collection of exosomes containing empty/516/516+RVG plasmids 12th: We subcultured four 225cm2 flasks of 293T cells.
13th: We subcultured sixteen 225cm2 flasks of 293T cells.
15th: We transfected 293T cells with plasmids (empty/516/516+RVG) and changed the culture media 6 hours after transfection.
17th: We collected culture media. Meanwhile we soaked centrifuge tubes which then be used in ultracentrifugation overnight in DEPC solution(1:1000).
18th: We separated exosomes by ultracentrifugation and stored the exosome solution at 4℃.
19th: We examined protein concentration of exosomes collected on 18th August(empty, 516,516+RVG).
 Pre-experiments for exosomes co-culture experiment. 15th: We subcultured HepG2 cells into a 12-well format.
16th: We transfected HepG2 cells with HBsAg plasmids and cluture medium was contaminated. So we subcultured HepG2 cells into a 12-well format again.
17th: We transfected HepG2 cells with HBsAg plasmids.
18th: We added 467 exosomes into culture media 18 hours after transfection and then collected HepG2 cells 12 hours after transfection and preserved them in Trizol.
19th: We extracted RNA from HepG2 cells. RT-PCR and Q-OCR the it.
 Others: 15th: We did RT-PCR, Q-PCR to obtain standard curves of 467 siRNA and 516 siRNA.
17th: We subcultured 293T cells.

WEEK 14 19th-25th, August

RVG targeting experiment 19th:We practised mouse tail intravenous injection.
20th: We practised mouse tail intravenous injection.
21th: We dosed 9 mice with exosomes (empty*3, 516,*3516+RVG*3) by tail intravenous injection.
22th: We anatomized C57 mice and collected the brain, heart, liver, spleen, lung, kidney and blood of them and preserved these tissues at -80℃.
23th: We extracted RNA from brain and serum we collected on 22th August. Then We did RT-PCR with the RNA.
24th: We did Q-PCR with the cDNA we got on 23th August.
 Absolute quantification of exosomes (empty, 516,516+RVG) 20th: We extracted RNA from exosomes (empty, 516,516+RVG) and did RT-PCR with the RNA.
 Others: 20th: We subcultured HepG2 cells.
21th: We subcultured 293T cells.

September

2013

WEEK 15 26th August-1th September

Redoing the experiment on 23th August 31th: We extract RNA from brain and serum we collected on 22th August.
1th: We did RT-PCR, Q-PCR with the RNA we extracted on 31th August.

WEEK 16-17 2th-11th, September

Exosomes co-culture experiment 31th: We subcultured HepG2 cells into 12-well format.
1th: We transfected HepG2 cells with HBsAg overexpression plasmids and changed transfection media with culture medium 6 hours after transfection.
2th: We added 467 exosomes to the culture medium 18 hours after transfection.
3th: We extracted RNA from HepG2 cells we transfected on 1th September and used the RNA to do RT-PCR and Q-PCR.
4th: We redid RT-PCR and Q-PCR on 3th September.
 Exosomes collection 4th: We transfected 293T cells with 467 plasmids.
5th: We soaked centrifuge tubes which then be used in ultracentrifugation overnight in DEPC solution(1:1000).
6th: We collected culture medium and separated exosomes by ultracentrifugation and stored the exosome solution at 4℃.
 Construction of standardized plasmid 1th: We transformated E.coli DH5α Competent Cells with pSB1C3 plasmids and spread these cells on the surface of solid LB medium added chloromycetin.
2th: We transferred single colony into fluid LB culture medium with chloromycetin, and shaken the medium overnight at 37℃.
3th: We extracted plasmids from culture medium shaken on 2th September and examined the DNA concentration of plasmids. Then we digested plasmids with XbaⅠ enzyme and SpeⅠenzyme. We did agarose gel electrophoriesis to test the effect of enzyme digestion. To get more pSB1C3 plasmids, we shaken E.coli DH5α Competent Cells containing pSB1C3 plasmids in fluid LB culture medium overnight at 37℃.
4th: We extracted plasmids from fluid LB culture medium shaken on 4th September.
5th: We digested a lot of pSB1C3 plasmids we extracted on 3th September with XbaⅠ enzyme and SpeⅠenzyme and did agarose gel electrophoriesis to recycle carrier segment by gel extraction kit.
6th: We digested a lot of pSB1C3 plasmids we extracted on 4th September with XbaⅠ enzyme and SpeⅠenzyme and did agarose gel electrophoriesis to recycle carrier segment by gel extraction kit. We linked carrier segment we got on 5th with 467 double-strand segment and 516 double-strand segment by T4 DNA ligase.
7th: We transformated E.coli DH5α Competent Cells with recombined plasmids we got on 6th September and spread these cells on the surface of solid LB medium added chloromycetin.
8th: We transferred single colony of recombination plasmids-containing E.coli cells into fluid LB culture medium with chloromycetin, and shaken the medium overnight at 37℃.
9th: We extracted plasmids from the LB culture medium we shaken on 8th September and sent the recombined plasmids sample to GenScript for sequencing.
10th:
11th: We got result of sequencing from GenScript. We constructed standardized 467-plasmid successfully.

October

2013

Week 1 12th-19th, October

12th : Subcultured 293T cells to six 225 cm2 flasks and three 75 cm2 flasks .
14th：Transferred 293T cells with plasmids and microRNA.For the six 225cm2 flasks , three groups : lipo*2, mirco162 RNA*2, micro162 RNA + GP120 plasmid(targeting to T cell) *26 hours After transfecting, Changed the culture mediaSubcultured 293T cells.
15th : Soaked centrifuge tubes which will be used in ultracentrifugation over night in ddH2O
16th: Collected 36-hour~48-hour culture containing exosomes.(The cells transfected with micro162 were contaminated by bacterium). Did pre-centrifuge(1500g:10min; 10000g: 30min). Separated exosomes by ultracentrifugation. Examine protein concentration of exosomes.Subcultured 293T cells.
17th: Separated T cells from the spleen of mouse, cultured the cells in 24-well plate, Each well contained 10^5 cells. cocultured empty exosomes and mirco162+GP120 exosomes with T cell respectively, each well added 10ug exosomes.Cultured HepG2 cells to 15 wells in 96-well plate, and did 4 plates.
18th : collected T cell in 12-well plate, separated CD4+ cells and CD4- cells using CD4+ T cell isolation Kit ,and started to extract RNA from the cells respectively, and then RT-Q-PCR.Subcultured 293T cells.HepG2 cells were contaminated by bacterium.
19th : Analyzed data.

Week 2 20th-26th, October

20th : Subcultured 293T cells
22th : transferred 293T cells with plasmids and microRNA(before transfecting, collected the medium for empty exosomes).For twelve 225 cm2 flasks, micro162 RNA*2, micro162 RNA+ GP120 plasmid *2, GFP inhibit siRNA *8; For twenty four 75 cm2 flasks, GFP inhibit siRNA + pres1 plasmid;cultured HepG2 cells to 15 wells in 96-well plate, and did 5 plates.
23th : Separated T cells from the spleen of mouse, cultured the cells in 24-well plate, Each well contained 3.2 *10^5 cells. (0 hours after adding exosomes into HepG2 cells) collected the medium of one plate with HepG2 cells for elisa. And Added 10ul CCK reagent and put the plate in incubator for 3hours, then tested it’s OD value. Add exosomes into HepG2 cells in each plate of the remaining four: PBS 10ul each well *5; empty exosomes 10ul(3ug) each well *5; micro162+GP120 exosomes 10ul(3ug) each well *5; Soaked centrifuge tubes which will be used in ultracentrifugation over night in ddH2O
24th : Collected 36-hour~48-hour culture containing exosomes.Cocultured empty exosomes, mirco162 exosomes and mirco162+GP120 exosomes with T cell respectively, each well added 10ug exosomes.12 hours after adding exosomes into HepG2 cells, collected the medium for elisa. Added 10ul CCK reagent and put the plate in incubator for 3hours, then tested it’s OD value. For 24/36/48 hours after adding exosomes into HepG2 cells, did the same experiments as 0/12hours.
25th : Collected T cell in 12-well plate, separated CD4+ cells and CD4- cells using CD4+ T cell isolation Kit ,and started to extract RNA from the cells respectively, and then RT-Q-PCR.Got the OD value of 0/12/24/36/48 hours after adding exosomes in HepG2 cells. Injected three GFP mice with empty exosomes , exosomes containing GFP inhibit siRNA, and pres1-exosomes with GFP inhibit siRNA respectively twice. For the first time at 9 am and the second time at 9 pm.
26th : Analyzed data
Killed the three GFP mice and took out their liver respectively at 9 am.
Did a frozen section of the hepatic tissue.
Observed the slice of the tissue with the fluorescence microscope and took pictures.
Using the Human IL-6 Elisa kit, Human IL-8 Elisa kit and Human TNF-α Elisa kit to test OD450 value of the medium we collected 0/12/24/36/48 hours after adding exosomes in HepG2 cells.
Analyzed data.

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