Answers.Body: <p>As shown in figure 1 of that paper, the anchor sequence is additional sequence that is added to the end of the polyT primer that provides a known and non-target binding site for additional PCR reactions. I gave <a href="https://f1000research.com/slides/7-251" rel="nofollow noreferrer">a presentation</a> about a month ago about the process that Oxford Nanopore Technology use in their strand-switching cDNA kit, which may be useful for understanding the process used by Tang <em>et al.</em>. Here are my strand-switch/PCR images from that presentation:</p>
  
  <ol>
  <li>PolyT primer addition, with mismatched anchor sequence</li>
  </ol>
  
  <p><a href="https://i.sstatic.net/rpSO9.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/rpSO9.png" alt="PolyT primer addition, with mismatched anchor sequence"></a></p>
  
  <ol start="2">
  <li>Strand switch primer addition, with overhanging anchor sequence</li>
  </ol>
  
  <p><a href="https://i.sstatic.net/lK3qh.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/lK3qh.png" alt="Strand switch primer addition, with overhanging anchor sequence"></a></p>
  
  <ol start="3">
  <li>PCR amplification, using primers that are complementary to the anchor sequences</li>
  </ol>
  
  <p><a href="https://i.sstatic.net/QnIow.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/QnIow.png" alt="PCR amplification using complementary primers"></a></p>
  
  <p>In the case of the Tang <em>et al.</em> paper, they use a polyA-tailing method for strand-switching, but the process is essentially the same.</p>
  
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Answers.Text: So is it basically a sequence added after the Poly(T) tail, which does not bind to the Poly(A) tail? If so, the main purpose of it is to provide a binding site for the PCR primers?
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Answers.Text: That's basically correct. It's not "added after", it's part of the same sequence.
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Body: <p>I am reading Tang et al. (2009).</p>
  
  <p>In the method description it is stated that:</p>
  
  <blockquote>
    <p>A single cell is manually picked under a microscope and lysed. Then mRNAs are reverse-transcribed into cDNAs using a poly(T) primer <strong>with anchor sequence</strong> (UP1) and unused primers are digested.</p>
  </blockquote>
  
  <p>What is an anchor sequence in this case?</p>
  
  <ol>
  <li>Tang, F. et al. <a href="https://www.nature.com/articles/nmeth.1315" rel="nofollow noreferrer">mRNA-Seq whole-transcriptome analysis of a single cell</a>. Nat. Methods 6, 377–382 (2009).</li>
  </ol>
  
Tags: <scrnaseq><primer>
Title: What is a poly(T) primer anchor sequence?
ThreadText: # What is a poly(T) primer anchor sequence?
  
  (Asked by: username_0 on 2018-04-05)
  
  I am reading Tang et al. (2009).
  
  In the method description it is stated that:
  
  > A single cell is manually picked under a microscope and lysed. Then mRNAs are reverse-transcribed into cDNAs using a poly(T) primer **with anchor sequence** (UP1) and unused primers are digested.
  
  What is an anchor sequence in this case?
  
  1. Tang, F. et al. [mRNA-Seq whole-transcriptome analysis of a single cell](https://www.nature.com/articles/nmeth.1315). Nat. Methods 6, 377–382 (2009).
  
  **Tags:** scrnaseq, primer
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-04-05. Score: 4 | Accepted answer
  
  As shown in figure 1 of that paper, the anchor sequence is additional sequence that is added to the end of the polyT primer that provides a known and non-target binding site for additional PCR reactions. I gave [a presentation](https://f1000research.com/slides/7-251) about a month ago about the process that Oxford Nanopore Technology use in their strand-switching cDNA kit, which may be useful for understanding the process used by Tang *et al.*. Here are my strand-switch/PCR images from that presentation:
  
  1. PolyT primer addition, with mismatched anchor sequence
  
  [![PolyT primer addition, with mismatched anchor sequence](https://i.sstatic.net/rpSO9.png)](https://i.sstatic.net/rpSO9.png)
  
  2. Strand switch primer addition, with overhanging anchor sequence
  
  [![Strand switch primer addition, with overhanging anchor sequence](https://i.sstatic.net/lK3qh.png)](https://i.sstatic.net/lK3qh.png)
  
  3. PCR amplification, using primers that are complementary to the anchor sequences
  
  [![PCR amplification using complementary primers](https://i.sstatic.net/QnIow.png)](https://i.sstatic.net/QnIow.png)
  
  In the case of the Tang *et al.* paper, they use a polyA-tailing method for strand-switching, but the process is essentially the same.
  
  > **Comments:**
  > **username_0**: So is it basically a sequence added after the Poly(T) tail, which does not bind to the Poly(A) tail? If so, the main purpose of it is to provide a binding site for the PCR primers?  
  > **username_1**: That's basically correct. It's not "added after", it's part of the same sequence.  
  
  ---
  
  