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LiangShaw · Oct 18, 2024 · 9559d65 · 9559d65
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diff --git a/2024/10/09/wetlab-CoIP/Co-IP_graph.png b/2024/10/09/wetlab-CoIP/Co-IP_graph.png
diff --git a/2024/10/09/wetlab-CoIP/index.html b/2024/10/09/wetlab-CoIP/index.html
@@ -5,7 +5,9 @@
 <head>
     <meta charset="utf-8">
     <meta name="keywords" content="wetlab-CoIPw, Shaw">
-    <meta name="description" content="">
+    <meta name="description" content="Co-IP  Procedure (from XGD)(1)    Preparing magnetic beads (for 6-well plate)
+
+Aliquot 7 µl of Protein A beads (mouse an">
     <meta http-equiv="X-UA-Compatible" content="IE=edge">
     <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=no">
     <meta name="renderer" content="webkit|ie-stand|ie-comp">
@@ -389,7 +391,7 @@ <h1 class="description center-align post-title">wetlab-CoIPw</h1>
 
                 <div class="post-date info-break-policy">
                     <i class="far fa-calendar-check fa-fw"></i>更新日期:&nbsp;&nbsp;
-                    2024-10-09
+                    2024-10-18
                 </div>
 
 
@@ -411,7 +413,33 @@ <h1 class="description center-align post-title">wetlab-CoIPw</h1>
 
         <div class="card-content article-card-content">
             <div id="articleContent">
-
+                <p>Co-IP  Procedure (from XGD)<br>(1)    Preparing magnetic beads (for 6-well plate)</p>
+<ol>
+<li>Aliquot 7 µl of Protein A beads (mouse antibody) to each 1.5 ml microfuge tube. </li>
+<li>Wash beads once with 0.5 ml of Low salt wash Buffer; 4 °C, 4,000 g, 2 min, discard supernatant.</li>
+<li>Resuspend beads with 0.5 ml Blocking Buffer, Block beads for at least 4 hours or overnight at 4 °C on a rotator. </li>
+<li>Wash beads once with 0.5 ml of Low salt wash Buffer, 10 min at 4 °C on a rotator; 4 °C, 4,000 g, 2 min, discard supernatant.</li>
+</ol>
+<p>(2) Preparing cell lysate (for 6-well plate)</p>
+<ol>
+<li>Wash cells once with 0.5 ml of PBS.</li>
+<li>200 uL of Nondenatured Lysis Buffer per sample, resuspend cells and incubate 60 min at 4 °C on a rotator.</li>
+<li>4 °C, 12,000 rpm, 10 min, transfer supernatant into new 1.5 ml microfuge tube.</li>
+<li>Add 1ug antibody to 200 ul lysate, at least 4 hours or overnight at 4 °C on a rotator.</li>
+</ol>
+<p>(3) Preparing Co-IP (for 6-well plate)</p>
+<ol>
+<li>Lysate (incubated antibody) add into protein A beads of blocked.</li>
+<li>Incubate overnight at 4 °C on a rotator.</li>
+</ol>
+<p>(4) Wash (for 6-well plate)</p>
+<ol>
+<li>4 °C, 4,000 g, 2 min, discard supernatant.</li>
+<li>Wash beads 3 times(or twice) with 0.5 ml of Low salt wash Buffer, 10 min at 4 °C on a rotator; 4 °C, 4,000 g, 2 min, discard supernatant.</li>
+<li>add 30 ul 1 x SDS elution buffer per sample, resuspend beads, 100 °C, 10 min.</li>
+<li>Cool to room temperature, save in -80 °C.</li>
+</ol>
+<img src="wetlab-CoIP/Co-IP_graph.png" width="400">
 
             </div>
             <hr/>

diff --git a/2024/10/14/Bioinfo-multi-sequence-align/Sequence_manipulate_suite_submit.png b/2024/10/14/Bioinfo-multi-sequence-align/Sequence_manipulate_suite_submit.png
diff --git a/2024/10/14/Bioinfo-multi-sequence-align/index.html b/2024/10/14/Bioinfo-multi-sequence-align/index.html
@@ -416,14 +416,16 @@ <h1 class="description center-align post-title">Bioinfo.multi-sequence-align</h1
 <h2 id="基因在物种间的保守性"><a href="#基因在物种间的保守性" class="headerlink" title="基因在物种间的保守性"></a><strong>基因在物种间的保守性</strong></h2><p>如果是well-known的基因，保守性大概了解，可以自行判断是使用核苷酸序列（非常保守时使用）还是氨基酸序列（不怎么保守时使用）。</p>
 <p>如果未知，可以通过以下途径知晓：</p>
 <ul>
-<li><a href="">blast/blastp</a>，可以直接用human里面该基因的序列进行blast/blastp比对，查看比对到有哪些物种。</li>
+<li><a target="_blank" rel="noopener" href="https://blast.ncbi.nlm.nih.gov/Blast.cgi">blast/blastp</a>，可以直接用human里面该基因的序列进行blast/blastp比对，查看比对到有哪些物种。</li>
 <li><a target="_blank" rel="noopener" href="https://www.orthodb.org/">OrthoDB</a>. 在OrthoDB用基因名查询。</li>
 </ul>
 <h2 id="获取物种进化关系"><a href="#获取物种进化关系" class="headerlink" title="获取物种进化关系"></a><strong>获取物种进化关系</strong></h2><p>如果你想显示有哪些物种，可以使用<a target="_blank" rel="noopener" href="http://www.timetree.org/">TimeTree</a>绘制指定物种间的进化树。</p>
 <h2 id="多条序列比较"><a href="#多条序列比较" class="headerlink" title="多条序列比较"></a><strong>多条序列比较</strong></h2><p>确定要比较的物种，获取这些物种SF3B1的序列，用 snapGene 进行多序列比对。<br>多比对的结果 export为fasta格式。  </p>
 <p>！！！如果比对结果中，个别地方有碱基的错位，可手动编辑fasta文件，进行修改。</p>
 <h2 id="比对结果可视化"><a href="#比对结果可视化" class="headerlink" title="比对结果可视化"></a><strong>比对结果可视化</strong></h2><p>下面提供一个在线的简单可视化工具：<a target="_blank" rel="noopener" href="https://www.detaibio.com/sms2/color_align_cons.html">碱基顺序比对工具</a>  </p>
 <p>将比对结果fasta文件输入后，submit，出现的结果，可点击鼠标右键，直接打印输出为PDF文件。或者复制存储为其他类型文件。</p>
+<img src="Bioinfo-multi-sequence-align/Sequence_manipulate_suite_submit.png" width="600">
+
 <h2 id="序列进化树"><a href="#序列进化树" class="headerlink" title="序列进化树"></a>序列进化树</h2><p>待更新…</p>
 
 

diff --git a/about/index.html b/about/index.html
@@ -622,19 +622,19 @@ <h1 id="教育经历"><a href="#教育经历" class="headerlink" title="教育
 <li><p>本科 武汉大学 生物技术</p>
 </li>
 </ul>
-<h1 id="指导教师"><a href="#指导教师" class="headerlink" title="指导教师"></a>指导教师</h1><p><a target="_blank" rel="noopener" href="http://bio.whu.edu.cn/info/1498/9424.htm"><strong>徐永镇</strong>(YongZhen Xu) 教授</a><br><a target="_blank" rel="noopener" href="https://xu-lab-whu.github.io/">XuLab Link</a></p>
+<h1 id="博士导师"><a href="#博士导师" class="headerlink" title="博士导师"></a>博士导师</h1><p><a target="_blank" rel="noopener" href="http://bio.whu.edu.cn/info/1498/9424.htm"><strong>徐永镇</strong>(YongZhen Xu) 教授</a><br><a target="_blank" rel="noopener" href="https://xu-lab-whu.github.io/">XuLab Link</a></p>
 <h1 id="个人技能"><a href="#个人技能" class="headerlink" title="个人技能"></a>个人技能</h1><ul>
 <li><strong>python</strong></li>
 <li><strong>R and related toolkits</strong></li>
 <li><strong>Linux</strong></li>
-<li><strong>AI draw</strong></li>
+<li><strong>Illustrator</strong></li>
 <li>et al.</li>
 </ul>
 <h1 id="目前涉猎"><a href="#目前涉猎" class="headerlink" title="目前涉猎"></a>目前涉猎</h1><ul>
-<li>概率论与数理统计</li>
-<li>深度学习(pytorch)</li>
-<li>网页内容抓取(scrapy)</li>
 <li>single cell analysis</li>
+<li>RNA binding protein</li>
+<li>Cas9-based functional screening</li>
+<li>…</li>
 </ul>
 <h1 id="联系方式"><a href="#联系方式" class="headerlink" title="联系方式"></a>联系方式</h1><ul>
 <li>邮箱<ul>
@@ -643,6 +643,10 @@ <h1 id="联系方式"><a href="#联系方式" class="headerlink" title="联系
 </ul>
 </li>
 </ul>
+<h1 id="学术成果"><a href="#学术成果" class="headerlink" title="学术成果"></a>学术成果</h1><ol>
+<li>   Chen-Hui Li#, <font color="red"><strong>Shao-Bo Liang#</strong></font>, Qi-Wei Huang, Zhen-Zhen Zhou, Zhan Ding, Ni Long, Kwang-Chon Wi, Liang Li, Xi-Ping Jiang, Yu-Jie Fan, and Yong-Zhen Xu*. (2024) <a target="_blank" rel="noopener" href="https://onlinelibrary.wiley.com/doi/full/10.1002/advs.202307804">Minor Spliceosomal 65K/RNPC3 Interacts with ANKRD11 and Mediates HDAC3-Regulated Histone Deacetylation and Transcription</a>. Advanced Science, 11(29): 2307804</li>
+<li>   Xianhong Zhang#, <font color="red"><strong>Shao-Bo Liang#</strong></font>, Zhuoyun Yi#, Zhaohui Qiao, Bo Xu, Huichao Geng, Honghong Wang, Xinhua Yin, Mingliang Tang, Wanzhong Ge, Yong-Zhen Xu, Kaiwei Liang, Yu-Jie Fan*, Liang Chen*. (2024) <a href="">Global coupling of R-loops dynamics with RNA polymerase II modulates gene expression and early development of Drosophila</a>. Nucleic Acid Research, Accepted.</li>
+</ol>
 <hr>
 <p>与各位一同学习进步！开源万岁，成果共享  </p>
 <hr>

diff --git a/archives/2024/10/index.html b/archives/2024/10/index.html
@@ -472,7 +472,9 @@
                         <div class="card-content article-content">
                             <div class="summary block-with-text">
 
-
+                                    Co-IP  Procedure (from XGD)(1)    Preparing magnetic beads (for 6-well plate)
+
+Aliquot 7 µl of Protein A beads (mouse an
 
                             </div>
                             <div class="publish-info">

diff --git a/archives/2024/index.html b/archives/2024/index.html
@@ -472,7 +472,9 @@
                         <div class="card-content article-content">
                             <div class="summary block-with-text">
 
-
+                                    Co-IP  Procedure (from XGD)(1)    Preparing magnetic beads (for 6-well plate)
+
+Aliquot 7 µl of Protein A beads (mouse an
 
                             </div>
                             <div class="publish-info">

diff --git a/archives/index.html b/archives/index.html
@@ -472,7 +472,9 @@
                         <div class="card-content article-content">
                             <div class="summary block-with-text">
 
-
+                                    Co-IP  Procedure (from XGD)(1)    Preparing magnetic beads (for 6-well plate)
+
+Aliquot 7 µl of Protein A beads (mouse an
 
                             </div>
                             <div class="publish-info">

diff --git a/index.html b/index.html
@@ -580,6 +580,10 @@
                     <div class="card-content article-content">
                         <div class="summary block-with-text">
 
+                                Co-IP  Procedure (from XGD)(1)    Preparing magnetic beads (for 6-well plate)
+
+Aliquot 7 µl of Protein A beads (mouse an
+
                         </div>
                         <div class="publish-info">
                             <span class="publish-date">

diff --git a/tags/BiocManager/index.html b/tags/BiocManager/index.html
@@ -810,6 +810,15 @@
                 </a>
 
 
+                <a href="/tags/handbook/" title="handbook: 6">
+                    <span class="chip center-align waves-effect waves-light
+                             chip-default "
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+                        <span class="tag-length">6</span>
+                    </span>
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+
+
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@@ -837,15 +846,6 @@
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diff --git a/tags/CCK-8/index.html b/tags/CCK-8/index.html
@@ -810,6 +810,15 @@
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+                <a href="/tags/handbook/" title="handbook: 6">
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@@ -837,15 +846,6 @@
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diff --git a/tags/CLIP/index.html b/tags/CLIP/index.html
@@ -810,6 +810,15 @@
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@@ -837,15 +846,6 @@
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@@ -810,6 +810,15 @@
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@@ -810,6 +810,15 @@
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@@ -810,6 +810,15 @@
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@@ -837,15 +846,6 @@
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diff --git a/tags/Docker/index.html b/tags/Docker/index.html
@@ -810,6 +810,15 @@
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@@ -837,15 +846,6 @@
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