Answers.Body: <p>It's likely that they accomplished this by using the <a href="http://genome.ucsc.edu/cgi-bin/hgTables" rel="nofollow noreferrer">UCSC Table Browser</a> to:</p>
  
  <ol>
  <li>Find the loci of the two isoforms you mention</li>
  <li>Finding CpG islands (Group = Regulation, Track = CpG Islands) near those transcription start sites</li>
  <li>Design primers using Applied Biosystem's software</li>
  </ol>
  
  <p>Alternatively, they list the exact primers used in <a href="https://www.tandfonline.com/action/downloadTable?id=T1&amp;doi=10.4161%2Fepi.7.1.18753&amp;downloadType=CSV" rel="nofollow noreferrer">Table 1</a>.</p>
  
  <p>They don't detail exactly how they did it, so if you have specific questions it might be worth it to email the corresponding author</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-08-12T19:48:41.813Z
Answers.Text: thank you for the suggestion i would try it out and yes it would be better if i drop them a mail
Answers.UserDisplayName: kcm
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-08-12T14:20:55.387Z
Answers.LastActivityDate: 2019-08-12T14:20:55.387Z
Answers.UserDisplayName: James Hawley
Body: <p>Im quoting the methods which was used </p>
  
  <blockquote>
    <p>We performed a bioinformatics analysis to identify potential CpG
    islands in the genomic sequences of RANKL and OPG genes. The USCS
    Human Genome Browser public database (genome.ucsc.edu), the Primer
    Express software (available from Applied Biosystems), and CpG Island
    Explorer software (cpgie.sourceforge.net) were used to explore the
    nucleo- tide sequences surrounding de transcription start site (TSS)
    of RANKL isoforms I and II (NG_008990.1 Ref Seq Gene), and OPG
    (NG_012202.1 Ref Seq Gene). A (C + G)/total bases ratio</p>
    
    <blockquote>
      <p>0.5 and CpG observed/CpG expected ratio >0.6 were used as criteria.</p>
    </blockquote>
  </blockquote>
  
  <p>Im looking for the region which they have used </p>
  
  <p>This is the paper </p>
  
  <pre><code>"Role of DNA methylation in the regulation of the
  RANKL-OPG system in human bone"
  </code></pre>
  
  <p>I tried using ucsc to check the region but didn't get much. The idea is to find the region to design the primer for the same</p>
  
  <p>How can i get the region from ucsc ,the CpG island around the TSS of the above mentioned genes which are RANKL and OPG</p>
  
  <p>Any suggestion or help would be highly appreciated </p>
  
Tags: <methylation>
Title: DNA bioinformatic search and methylation analysis by qMSP
ThreadText: # DNA bioinformatic search and methylation analysis by qMSP
  
  (Asked by: username_0 on 2019-08-05)
  
  Im quoting the methods which was used
  
  > We performed a bioinformatics analysis to identify potential CpG
  > islands in the genomic sequences of RANKL and OPG genes. The USCS
  > Human Genome Browser public database (genome.ucsc.edu), the Primer
  > Express software (available from Applied Biosystems), and CpG Island
  > Explorer software (cpgie.sourceforge.net) were used to explore the
  > nucleo- tide sequences surrounding de transcription start site (TSS)
  > of RANKL isoforms I and II (NG\_008990.1 Ref Seq Gene), and OPG
  > (NG\_012202.1 Ref Seq Gene). A (C + G)/total bases ratio
  >
  > > 0.5 and CpG observed/CpG expected ratio >0.6 were used as criteria.
  
  Im looking for the region which they have used
  
  This is the paper
  
  ```
  "Role of DNA methylation in the regulation of the
  RANKL-OPG system in human bone"
  
  ```
  
  I tried using ucsc to check the region but didn't get much. The idea is to find the region to design the primer for the same
  
  How can i get the region from ucsc ,the CpG island around the TSS of the above mentioned genes which are RANKL and OPG
  
  Any suggestion or help would be highly appreciated
  
  **Tags:** methylation
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-08-12. Score: 1 | Accepted answer
  
  It's likely that they accomplished this by using the [UCSC Table Browser](http://genome.ucsc.edu/cgi-bin/hgTables) to:
  
  1. Find the loci of the two isoforms you mention
  2. Finding CpG islands (Group = Regulation, Track = CpG Islands) near those transcription start sites
  3. Design primers using Applied Biosystem's software
  
  Alternatively, they list the exact primers used in [Table 1](https://www.tandfonline.com/action/downloadTable?id=T1&doi=10.4161%2Fepi.7.1.18753&downloadType=CSV).
  
  They don't detail exactly how they did it, so if you have specific questions it might be worth it to email the corresponding author
  
  > **Comments:**
  > **username_0**: thank you for the suggestion i would try it out and yes it would be better if i drop them a mail  
  
  ---
  
  