Sandbox: Difference between revisions

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<html>
__TOC__
<head>
<style>
<!-- HIDE WIKI STUFF -->


#column-one { display:none; width:0px;}
.container{background-color: #ffffff; margin-top:0px}
.OWWNBcpCurrentDateFilled {display: none;}
#content {  width: 0px; margin: 0 auto auto 0;  padding: 0em 0em 0em 0em; align: center;}
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#globalWrapper{width:984px; background-color: #ffffff; margin-left: auto; margin-right: auto}
#column-one {display:none; width:0px;background-color: #ffffff;}
#content{ margin: 0 0 0 0; align: center; padding: 12px; width: 960px;background-color: #ffff; border: 0;}
#bodyContent{ width: 960px; align: center; background-color: #ffffff;}
#column-content{width: 984px;background-color: #ffff;}
#footer{display: none; position: center; width: 960px}
@media screen {
    body { background: #ffffff url(http://openwetware.org/images/1/14/Biomod-2012-utokyo-uthongo-wrapper-bg.jpg) repeat; }
}


</style>
----


<style>
== My Test of OpenWetWare Editing ==
I would like to try the following editing tasks:
* Add a [hyperlink](https://uk.yahoo.com/?ilc=400).
** For example: Link to the paper can be found HERE[http://www.nature.com/nature/journal/v403/n6767/pdf/403339a0.pdf].
* Add a document or Dropbox link:
** Addition of document: [[Image:Example.jpg]]
** Addition of Dropbox link: The file can be downloaded from Dropbox via this [LINK]
* Cite a paper.
** Hopefully see the list of references at the bottom of the page.
** This is a really interesting study <ref>Reference goes here</ref>
* Add a picture.


* {
== References ==
text-shadow: 0px 1px 2px #aaa;
{{Reflist}}
}


#bodyContent, #column-content, #content {
----
background: #ffffff url(http://openwetware.org/images/1/14/Biomod-2012-utokyo-uthongo-wrapper-bg.jpg) repeat;
}


#column-content {
'''EmbryoName HK023- chicken embryo- Stage 19.5 - 8.12.14'''
border-left: 1px solid #888;
border-right: 1px solid #888;
}


#header {
  width: 960px;
  height: 304px;
  background: url(http://openwetware.org/images/3/3b/Biomod-2012-UTokyo-UT-Hongo_header_test2.png) no-repeat;
  background-size: 100% auto;
  margin-bottom: 0px;
  padding: 0px 0px 0px 0px;
/*  border-bottom: 1px solid #DEDEDE; */
}


#menu {
==Experiment==
  display: block;
  width: 956px;
  padding: 0px;
  background-color: black;
  border: 2px solid #888;
  margin-bottom: 15px;
}


ul.menu li a {
'''Objective'''
  display: block;
To transform HB101s with a plasmid encoding GFP (called pGFP) and express this protein by inducing with arabinose. Testing out openwetware
/*  border: 1px solid #474655; */
'''Procedure'''
  padding: 8px 10px;
  text-decoration: none;
/*  color: #333; */
  color: #fff;
/*  width: 121px;  */
  margin: 0px;
  text-align: center;
  font-size: large;
}


ul.menu li a:hover{
* Trigeminal nerve bilaterally DiO crystals
  color: cyan;
* 7th/8th nerve bilaterally DiI crystals (Big chunk on 7th nerve on L side and big chunk on 8th on R side)
}


ul.menu {
'''Notes'''
/*  display: none;
No obvious contamination, purposelly put a greater chunk of dye on the 7th nerve on the L side and the 8th nerve on the R side so will see if there is any visible difference between the amount of neurons labelled in different positions within the rhombomere.  
  position: absolute; */
  height: 40px;
  margin:0;
  padding:0;
  list-style:none;
  float: center;
}


ul.menu li {
==Files==
/*  display:inline;*/
  margin:0;
  padding:6px;
  float: left;
  position: relative;
}


ul.menu li:hover ul {
*
  display: block;
*
  position: absolute;
*
  z-index: 100;
*
}


ul.submenu {
*
  display: none;
** abd dfg
  list-style: none;
**
  background-color: #f0f0f0;
  border: 1px solid #ccc;
}


ul.submenu li {
==Results==
  float: none;
  margin: 0px;
}


ul.submenu li a {
===Facial===
  text-align: left;
(Green)
  margin: 0px;
  width: 340px;
  padding: 0 0 0 12px;
  color: black;
  text-decoration: none;
  font-size: large
}


ul.submenu li a:hover {
* '''''Afferents'''''
   color: black;
    
  text-decoration: underline;
}


.thumb {
* '''''Efferents'''''
  border-image: url(http://openwetware.org/images/1/14/Biomod-2012-utokyo-uthongo-wrapper-bg.jpg) repeat;
}


.mytable {
  border-image: url(http://openwetware.org/images/1/14/Biomod-2012-utokyo-uthongo-wrapper-bg.jpg) repeat;
}


</style>
</head>
<body>


  <div style="text-align: right">
    <p><a href="http://openwetware.org/index.php?title=Template:Biomod/2012/UTokyo/UT-Hongo&action=edit">edit this header</a></p>
  </div>


  <div style="height: 60px; margin-bottom: 18px;">
    <div style="float: left; width: 250px; padding: 3px; background-color: white;">
      <a href="http://biomod.net/"><img src="http://openwetware.org/images/8/82/Biomod2012-logo.png" width="250px" height="50px"></img></a>
    </div>
    <div style="float: right; width: 240px; padding: 3px; background-color: white;">
      <a href="http://www.u-tokyo.ac.jp/en/" target="_blank"><img src="http://www.u-tokyo.ac.jp/en/images/banner/UT-logo.gif" width="234" height="60" border="0" alt="The University of Tokyo"></img></a>
    </div>
  </div>


    <div id="header">
    </div>


    <div id="menu">
===VIII ===
      <ul class="menu">
(green)
<li class="toppage"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo">Top</a></li>
<li class="motives"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Intro">Motives</a></li>
<!-- <li class="design"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Function">Design</a></li> -->
<li class="result"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly">Design & Results</a>
  <ul class="submenu">
    <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Assembly_of_the_DNA_Shell">Assembly of the DNA Shell</a></li>
    <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Capturing_ability">Capturing Ability</a></li>
    <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Immobilizing_on_microfluidic_device">Immobilizing on microfluidic device</a></li>
    <li><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Assembly#Supporting_Enzyme">Supporting Enzyme</a></li>
  </ul>
</li>
<li class="method"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Method">Method</a></li>
<li class="futurework"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/FutureWork">Progress & Beyond</a></li>
<li class="team"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Team">Team</a></li>
<li class="acknowledgement"><a href="/wiki/Biomod/2012/UTokyo/UT-Hongo/Acknowledgement">Acknowledgement</a></li>
      </ul>
    </div>


</body>
* '''''Afferents'''''
</html>
 
 
 
* '''''Efferents'''''
 
 
* '''''Other'''''
 
 
 
===Basal plate ===
(red)
 
 
==Summary==
 
'''Questions'''
 
'''Future'''
 
 
<META HTTP-EQUIV="refresh" CONTENT="10;URL=http://my.newplace.com/">
 
 
Mary {pad|4em} had a little lamb.
 
'''Badrul Arefin'''
 
 
# Jeong M^, {{spaces|7}} <u>Sun D^</u>, Luo M^, Huang Y, Challen GA, <u>Rodriguez B</u>, Zhang X, Chavez L, Wang H, Hannah R, Kim S, Yang L, Ko M, Chen R, Gottgens B, Lee JS, Gunaratne P, Godley LA, Darlington GJ, Rao A, <u>Li W*</u>, Goodell MA*: Large conserved domains of low DNA methylation maintained by Dnmt3a. <br/> '''''          Nature Genetics''''' . Accepted.
# <u>Akdemir KC</u>, Jain AK, Alton K, Arronow B, J. CA, ..., <u>Li W*</u>, Barton MC*: Genome Wide Profiling Reveals Stimulus-specific Functions of p53 During Differentiation and DNA Damage of Human Embryonic Stem Cells. <br/>'''''Nucleic Acids Res.''''' Accepted
# Klein JB, Piao L, …, <u>Li W</u>, Shi X, Kutateladze TG: KDM5B demethylase binds to its histone target and the product through distinct modules.<br/>''Cell Reports''. Accepted. <br/><br/>'''2013''' <br/><br/>
# <u>Chen K</u>, <u>Xi Y</u>, Pan X, Dent S, He X, <u>Li W*</u>: DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing. <br/>'''''Genome Res.''''' 23 (2013) 341-351. [http://www.bcm.edu/news/item.cfm?newsID=6723 BCM News];  [http://epigenie.com/danpos-reveals-dynamic-nucleosomes Epigenie Headline]  <br/><br/>
# <u>Wang L</u>, <u>Park JH</u>, Wang S, Kocher JP, <u>Li W*</u>: CPAT: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model. <br/>'''''Nucleic Acids Res.''''' 41 (2013) e74.<br/><br/>
# <u>Lin X</u>, <u>Sun D</u>, <u>Rodriguez B</u>, Zhao Q, Sun H, Zhang Y, <u>Li W*</u>: BseQC: Quality Control of bisulfite sequencing experiments. <br/>'''''Bioinformatics''''' 29 (2013) 3227-3229. PMCID: PMC3842756 .<br/><br/>
# <u>Chen K^</u>, Wilson MA^, Hirsch C, Watson A, Liang S, Lu Y, <u>Li W*</u>, Dent S*: Stabilization of the Promoter Nucleosomes in Nucleosome Free Region by the Yeast Ssn6-Tup1 Corepressor. <br/>'''''Genome Res.''''' 23 (2013) 312-322. <br/><br/>

Revision as of 21:58, 6 March 2016


My Test of OpenWetWare Editing

I would like to try the following editing tasks:

  • Add a [hyperlink](https://uk.yahoo.com/?ilc=400).
    • For example: Link to the paper can be found HERE[1].
  • Add a document or Dropbox link:
    • Addition of document:
    • Addition of Dropbox link: The file can be downloaded from Dropbox via this [LINK]
  • Cite a paper.
    • Hopefully see the list of references at the bottom of the page.
    • This is a really interesting study [1]
  • Add a picture.

References

  1. ↑ Reference goes here

EmbryoName HK023- chicken embryo- Stage 19.5 - 8.12.14


Experiment

Objective To transform HB101s with a plasmid encoding GFP (called pGFP) and express this protein by inducing with arabinose. Testing out openwetware Procedure

  • Trigeminal nerve bilaterally DiO crystals
  • 7th/8th nerve bilaterally DiI crystals (Big chunk on 7th nerve on L side and big chunk on 8th on R side)

Notes No obvious contamination, purposelly put a greater chunk of dye on the 7th nerve on the L side and the 8th nerve on the R side so will see if there is any visible difference between the amount of neurons labelled in different positions within the rhombomere.

Files

    • abd dfg

Results

Facial

(Green)

  • Afferents


  • Efferents




VIII

(green)

  • Afferents


  • Efferents


  • Other


Basal plate

(red)


Summary

Questions

Future


<META HTTP-EQUIV="refresh" CONTENT="10;URL=http://my.newplace.com/">


Mary {pad|4em} had a little lamb.

Badrul Arefin


  1. Jeong M^, Template:Spaces Sun D^, Luo M^, Huang Y, Challen GA, Rodriguez B, Zhang X, Chavez L, Wang H, Hannah R, Kim S, Yang L, Ko M, Chen R, Gottgens B, Lee JS, Gunaratne P, Godley LA, Darlington GJ, Rao A, Li W*, Goodell MA*: Large conserved domains of low DNA methylation maintained by Dnmt3a.
    Nature Genetics . Accepted.
  2. Akdemir KC, Jain AK, Alton K, Arronow B, J. CA, ..., Li W*, Barton MC*: Genome Wide Profiling Reveals Stimulus-specific Functions of p53 During Differentiation and DNA Damage of Human Embryonic Stem Cells.
    Nucleic Acids Res. Accepted
  3. Klein JB, Piao L, …, Li W, Shi X, Kutateladze TG: KDM5B demethylase binds to its histone target and the product through distinct modules.
    Cell Reports. Accepted.

    2013

  4. Chen K, Xi Y, Pan X, Dent S, He X, Li W*: DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing.
    Genome Res. 23 (2013) 341-351. BCM News; Epigenie Headline

  5. Wang L, Park JH, Wang S, Kocher JP, Li W*: CPAT: Coding-Potential Assessment Tool Using an Alignment-Free Logistic Regression Model.
    Nucleic Acids Res. 41 (2013) e74.

  6. Lin X, Sun D, Rodriguez B, Zhao Q, Sun H, Zhang Y, Li W*: BseQC: Quality Control of bisulfite sequencing experiments.
    Bioinformatics 29 (2013) 3227-3229. PMCID: PMC3842756 .

  7. Chen K^, Wilson MA^, Hirsch C, Watson A, Liang S, Lu Y, Li W*, Dent S*: Stabilization of the Promoter Nucleosomes in Nucleosome Free Region by the Yeast Ssn6-Tup1 Corepressor.
    Genome Res. 23 (2013) 312-322.

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