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Created page with "<p><b>SOLiD</b> (Sequencing by Oligonucleotide Ligation and Detection) is a next-generation sequencing technology developed by <font color="#0645ad">Life Technologies</font> and ..."
<p><b>SOLiD</b> (Sequencing by Oligonucleotide Ligation and Detection) is a next-generation sequencing technology developed by <font color="#0645ad">Life Technologies</font> and has been commercially available since 2008. These next generation technologies generate hundreds of millions to billions of small sequence reads at one time. Well-known examples of such DNA sequencing methods include 454 <font color="#0645ad">pyrosequencing</font> (introduced in 2005, generating millions of 200-400bp reads in 2009), the <font color="#0645ad">Solexa</font> system (introduced in 2006, generating hundreds of millions of 50-100bp reads in 2009) and the SOLiD system (introduced in 2007, generating billions of 50bp reads in 2009). These methods have reduced the cost from $0.01/base in 2004 to nearly $0.0001/base in 2006 and increased the sequencing capacity from 1,000,000 bases/machine/day in 2004 to more than 5,000,000,000 bases/machine/day in 2009. Over 30 publications exist describing its use first for nucleosome positioning from Valouev et al.,<sup id="cite_ref-0" class="reference"><font size="2"><font color="#0645ad"><span>[</span>1<span>]</span></font></font></sup> transcriptional profiling or strand sensitive RNA-Seq with Cloonan et al.,<sup id="cite_ref-1" class="reference"><font size="2"><font color="#0645ad"><span>[</span>2<span>]</span></font></font></sup> single cell transcriptional profiling with Tang et al.<sup id="cite_ref-2" class="reference"><font size="2"><font color="#0645ad"><span>[</span>3<span>]</span></font></font></sup> and ultimately human resequencing with McKernan et al.<sup id="cite_ref-3" class="reference"><font size="2"><font color="#0645ad"><span>[</span>4<span>]</span></font></font></sup></p>
<p>
</p>
<h2><span id="Chemistry" class="mw-headline">Chemistry</span></h2>
<p>A library of DNA fragments is prepared from the sample to be sequenced, and are used to prepare clonal bead populations. That is, only one species of fragment will be present on the surface of each magnetic bead. The fragments attached to the magnetic beads will have a universal P1 adapter sequence attached so that the starting sequence of every fragment is both known and identical. Emulsion <font color="#0645ad">PCR</font> takes place in microreactors containing all the necessary reagents for PCR. The resulting PCR products attached to the beads are then covalently bound to a glass slide.</p>
<p>Primers hybridize to the P1 adapter sequence within the library template. A set of four fluorescently labeled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length. Following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles.</p>
<p>Five rounds of primer reset are completed for each sequence tag. Through the primer reset process, each base is interrogated in two independent ligation reactions by two different primers. For example, the base at read position 5 is assayed by primer number 2 in ligation cycle 2 and by primer number 3 in ligation cycle 1.</p>
<h2><span id="Throughput_and_Accuracy" class="mw-headline">Throughput and Accuracy</span></h2>
<p>According to ABI, the SOLiD 3plus platform yields 60 gigabases of usable DNA data per run. Due to the two base encoding system, an inherent accuracy check is built in to the technology and offers 99.94% accuracy. The chemistry of the systems also means that it is not hindered by homopolymers unlike the Roche 454 FLX system and so large and difficult homopolymer repeat regions are no longer a problem to sequence.</p>
<h2><span id="Applications" class="mw-headline">Applications</span></h2>
<p>Naturally the technology will be used to sequence DNA, but because of the high parallel nature of the all next generation technologies they also have applications in transcriptomics and epigenomics.</p>
<p>Microarrays have been the mainstay of the transcriptomics world for the last ten years and array based technology has branched out to other areas. But they are limited in that only information can be obtained for probes that are on the chip. Only information for organisms for which chips are available can obtained, and they come with all the problems of hybridizing large numbers of molecules (differing hybridizing temperatures).</p>
<p>Transcriptomics by next gen sequencing will mean these barriers no longer hold true. Any organism's entire transcriptome could be potentially sequenced in one run (for very small bacterial genomes) and not only would the identification of each transcript be available but expression profiling is possible as quantitative reads can also be achieved.</p>
<p>Chromatin immunoprecipitation (ChIP) is a method for determining transcription factor binding sites and DNA-protein interactions. It has in the past been combined with array technology (ChIP-chip) with some success. Next gen sequencing can also be applied in this area. Methylation immunoprecipitation (MeDIP) can also be performed and also on arrays.</p>
<p>The ability to learn more about methylation and TF binding sites on a genome wide scale is a valuable resource and could teach us much about disease and molecular biology in general.</p>
<h2><span id="See_also" class="mw-headline">See also</span></h2>
<ul>
<li><a title="2 Base Encoding" href="/wiki/2_Base_Encoding"><font color="#0645ad">2 Base Encoding</font></a></li>
<li><a class="mw-redirect" title="Next-generation sequencing" href="/wiki/Next-generation_sequencing"><font color="#0645ad">Next-generation sequencing</font></a></li>
<li><a title="Applied Biosystems" href="/wiki/Applied_Biosystems"><font color="#0645ad">Applied Biosystems</font></a></li>
<li><a title="Illumina (company)" href="/wiki/Illumina_(company)"><font color="#0645ad">Illumina (company)</font></a></li>
<li><a title="454 Life Sciences" href="/wiki/454_Life_Sciences"><font color="#0645ad">454 Life Sciences</font></a></li>
</ul>
<h2><span id="References" class="mw-headline">References</span></h2>
<div class="reflist references-small">
<div class="references">
<ol>
<li id="cite_note-0"><b><a href="#cite_ref-0"><font color="#0645ad">^</font></a></b> <span class="citation Journal">Valouev A, Ichikawa J, Tonthat T, <i>et al.</i> (July 2008). <a class="external text" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2493394" rel="nofollow"><font color="#3366bb">"A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning"</font></a>. <i>Genome Research</i> <b>18</b> (7): 1051–63. <a title="Digital object identifier" href="/wiki/Digital_object_identifier"><font color="#0645ad">doi</font></a>:<a class="external text" href="http://dx.doi.org/10.1101%2Fgr.076463.108" rel="nofollow"><font color="#3366bb">10.1101/gr.076463.108</font></a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a> <a class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/18477713" rel="nofollow"><font color="#3366bb">18477713</font></a>.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=A+high-resolution%2C+nucleosome+position+map+of+C.+elegans+reveals+a+lack+of+universal+sequence-dictated+positioning&rft.jtitle=Genome+Research&rft.aulast=Valouev+A%2C+Ichikawa+J%2C+Tonthat+T%2C+%27%27et+al.%27%27&rft.au=Valouev+A%2C+Ichikawa+J%2C+Tonthat+T%2C+%27%27et+al.%27%27&rft.date=July+2008&rft.volume=18&rft.issue=7&rft.pages=1051%E2%80%9363&rft_id=info:doi/10.1101%2Fgr.076463.108&rft_id=info:pmid/18477713&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"><span style="display: none"> </span></span></li>
<li id="cite_note-1"><b><a href="#cite_ref-1"><font color="#0645ad">^</font></a></b> <span class="citation Journal">Cloonan N, Forrest AR, Kolle G, <i>et al.</i> (July 2008). "Stem cell transcriptome profiling via massive-scale mRNA sequencing". <i>Nature Methods</i> <b>5</b> (7): 613–9. <a title="Digital object identifier" href="/wiki/Digital_object_identifier"><font color="#0645ad">doi</font></a>:<a class="external text" href="http://dx.doi.org/10.1038%2Fnmeth.1223" rel="nofollow"><font color="#3366bb">10.1038/nmeth.1223</font></a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a> <a class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/18516046" rel="nofollow"><font color="#3366bb">18516046</font></a>.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Stem+cell+transcriptome+profiling+via+massive-scale+mRNA+sequencing&rft.jtitle=Nature+Methods&rft.aulast=Cloonan+N%2C+Forrest+AR%2C+Kolle+G%2C+%27%27et+al.%27%27&rft.au=Cloonan+N%2C+Forrest+AR%2C+Kolle+G%2C+%27%27et+al.%27%27&rft.date=July+2008&rft.volume=5&rft.issue=7&rft.pages=613%E2%80%939&rft_id=info:doi/10.1038%2Fnmeth.1223&rft_id=info:pmid/18516046&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"><span style="display: none"> </span></span></li>
<li id="cite_note-2"><b><a href="#cite_ref-2"><font color="#0645ad">^</font></a></b> <span class="citation Journal">Tang F, Barbacioru C, Wang Y, <i>et al.</i> (May 2009). "mRNA-Seq whole-transcriptome analysis of a single cell". <i>Nature Methods</i> <b>6</b> (5): 377–82. <a title="Digital object identifier" href="/wiki/Digital_object_identifier"><font color="#0645ad">doi</font></a>:<a class="external text" href="http://dx.doi.org/10.1038%2Fnmeth.1315" rel="nofollow"><font color="#3366bb">10.1038/nmeth.1315</font></a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a> <a class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/19349980" rel="nofollow"><font color="#3366bb">19349980</font></a>.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=mRNA-Seq+whole-transcriptome+analysis+of+a+single+cell&rft.jtitle=Nature+Methods&rft.aulast=Tang+F%2C+Barbacioru+C%2C+Wang+Y%2C+%27%27et+al.%27%27&rft.au=Tang+F%2C+Barbacioru+C%2C+Wang+Y%2C+%27%27et+al.%27%27&rft.date=May+2009&rft.volume=6&rft.issue=5&rft.pages=377%E2%80%9382&rft_id=info:doi/10.1038%2Fnmeth.1315&rft_id=info:pmid/19349980&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"><span style="display: none"> </span></span></li>
<li id="cite_note-3"><b><a href="#cite_ref-3"><font color="#0645ad">^</font></a></b> <span class="citation Journal">McKernan KJ, Peckham HE, Costa GL, <i>et al.</i> (September 2009). <a class="external text" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2752135" rel="nofollow"><font color="#3366bb">"Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding"</font></a>. <i>Genome Research</i> <b>19</b> (9): 1527–41. <a title="Digital object identifier" href="/wiki/Digital_object_identifier"><font color="#0645ad">doi</font></a>:<a class="external text" href="http://dx.doi.org/10.1101%2Fgr.091868.109" rel="nofollow"><font color="#3366bb">10.1101/gr.091868.109</font></a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a> <a class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/19546169" rel="nofollow"><font color="#3366bb">19546169</font></a>.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Sequence+and+structural+variation+in+a+human+genome+uncovered+by+short-read%2C+massively+parallel+ligation+sequencing+using+two-base+encoding&rft.jtitle=Genome+Research&rft.aulast=McKernan+KJ%2C+Peckham+HE%2C+Costa+GL%2C+%27%27et+al.%27%27&rft.au=McKernan+KJ%2C+Peckham+HE%2C+Costa+GL%2C+%27%27et+al.%27%27&rft.date=September+2009&rft.volume=19&rft.issue=9&rft.pages=1527%E2%80%9341&rft_id=info:doi/10.1101%2Fgr.091868.109&rft_id=info:pmid/19546169&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"><span style="display: none"> </span></span></li>
</ol>
</div>
</div>
<h2><span id="Further_reading" class="mw-headline">Further reading</span></h2>
<ul>
<li><span class="citation Journal">Mardis ER (2008). "Next-generation DNA sequencing methods". <i>Annual Review of Genomics and Human Genetics</i> <b>9</b>: 387–402. <a title="Digital object identifier" href="/wiki/Digital_object_identifier"><font color="#0645ad">doi</font></a>:<a class="external text" href="http://dx.doi.org/10.1146%2Fannurev.genom.9.081307.164359" rel="nofollow"><font color="#3366bb">10.1146/annurev.genom.9.081307.164359</font></a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a> <a class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/18576944" rel="nofollow"><font color="#3366bb">18576944</font></a>.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Next-generation+DNA+sequencing+methods&rft.jtitle=Annual+Review+of+Genomics+and+Human+Genetics&rft.aulast=Mardis+ER&rft.au=Mardis+ER&rft.date=2008&rft.volume=9&rft.pages=387%E2%80%93402&rft_id=info:doi/10.1146%2Fannurev.genom.9.081307.164359&rft_id=info:pmid/18576944&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"><span style="display: none"> </span></span></li>
<li><span class="citation Journal">Mardis ER (2009). <a class="external text" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2684661" rel="nofollow"><font color="#3366bb">"New strategies and emerging technologies for massively parallel sequencing: applications in medical research"</font></a>. <i>Genome Medicine</i> <b>1</b> (4): 40. <a title="Digital object identifier" href="/wiki/Digital_object_identifier"><font color="#0645ad">doi</font></a>:<a class="external text" href="http://dx.doi.org/10.1186%2Fgm40" rel="nofollow"><font color="#3366bb">10.1186/gm40</font></a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a> <a class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/19435481" rel="nofollow"><font color="#3366bb">19435481</font></a>.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=New+strategies+and+emerging+technologies+for+massively+parallel+sequencing%3A+applications+in+medical+research&rft.jtitle=Genome+Medicine&rft.aulast=Mardis+ER&rft.au=Mardis+ER&rft.date=2009&rft.volume=1&rft.issue=4&rft.pages=40&rft_id=info:doi/10.1186%2Fgm40&rft_id=info:pmid/19435481&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"><span style="display: none"> </span></span></li>
</ul>
<h2><span id="External_links" class="mw-headline">External links</span></h2>
<ul>
<li><span class="citation web"><a class="external text" href="http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_061241.pdf" rel="nofollow"><font color="#3366bb">"The SOLiD 3 System: Enabling the Next Generation of Science"</font></a>. <a title="Life Technologies" href="/wiki/Life_Technologies"><font color="#0645ad">Life Technologies</font></a>. 2009<span class="printonly">. <a class="external free" href="http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_061241.pdf" rel="nofollow"><font color="#3366bb">http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_061241.pdf</font></a></span><span class="reference-accessdate">. Retrieved January 27, 2010</span>.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=bookitem&rft.btitle=The+SOLiD+3+System%3A+Enabling+the+Next+Generation+of+Science&rft.atitle=&rft.date=2009&rft.pub=%5B%5BLife+Technologies%5D%5D&rft_id=http%3A%2F%2Fwww3.appliedbiosystems.com%2Fcms%2Fgroups%2Fmcb_marketing%2Fdocuments%2Fgeneraldocuments%2Fcms_061241.pdf&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"><span style="display: none"> </span></span></li>
<li><span class="citation web"><a class="external text" href="http://marketing.appliedbiosystems.com/mk/get/SOLID_ACCURACY_Landing?CID=BN-88889-NAHomePage" rel="nofollow"><font color="#3366bb">"The SOLiD 3 Plus System"</font></a>. <a title="Life Technologies" href="/wiki/Life_Technologies"><font color="#0645ad">Life Technologies</font></a>. 2009<span class="printonly">. <a class="external free" href="http://marketing.appliedbiosystems.com/mk/get/SOLID_ACCURACY_Landing?CID=BN-88889-NAHomePage" rel="nofollow"><font color="#3366bb">http://marketing.appliedbiosystems.com/mk/get/SOLID_ACCURACY_Landing?CID=BN-88889-NAHomePage</font></a></span><span class="reference-accessdate">. Retrieved January 27, 2010</span>.</span></li>
</ul>
<p>
</p>
<h2><span id="Chemistry" class="mw-headline">Chemistry</span></h2>
<p>A library of DNA fragments is prepared from the sample to be sequenced, and are used to prepare clonal bead populations. That is, only one species of fragment will be present on the surface of each magnetic bead. The fragments attached to the magnetic beads will have a universal P1 adapter sequence attached so that the starting sequence of every fragment is both known and identical. Emulsion <font color="#0645ad">PCR</font> takes place in microreactors containing all the necessary reagents for PCR. The resulting PCR products attached to the beads are then covalently bound to a glass slide.</p>
<p>Primers hybridize to the P1 adapter sequence within the library template. A set of four fluorescently labeled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length. Following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles.</p>
<p>Five rounds of primer reset are completed for each sequence tag. Through the primer reset process, each base is interrogated in two independent ligation reactions by two different primers. For example, the base at read position 5 is assayed by primer number 2 in ligation cycle 2 and by primer number 3 in ligation cycle 1.</p>
<h2><span id="Throughput_and_Accuracy" class="mw-headline">Throughput and Accuracy</span></h2>
<p>According to ABI, the SOLiD 3plus platform yields 60 gigabases of usable DNA data per run. Due to the two base encoding system, an inherent accuracy check is built in to the technology and offers 99.94% accuracy. The chemistry of the systems also means that it is not hindered by homopolymers unlike the Roche 454 FLX system and so large and difficult homopolymer repeat regions are no longer a problem to sequence.</p>
<h2><span id="Applications" class="mw-headline">Applications</span></h2>
<p>Naturally the technology will be used to sequence DNA, but because of the high parallel nature of the all next generation technologies they also have applications in transcriptomics and epigenomics.</p>
<p>Microarrays have been the mainstay of the transcriptomics world for the last ten years and array based technology has branched out to other areas. But they are limited in that only information can be obtained for probes that are on the chip. Only information for organisms for which chips are available can obtained, and they come with all the problems of hybridizing large numbers of molecules (differing hybridizing temperatures).</p>
<p>Transcriptomics by next gen sequencing will mean these barriers no longer hold true. Any organism's entire transcriptome could be potentially sequenced in one run (for very small bacterial genomes) and not only would the identification of each transcript be available but expression profiling is possible as quantitative reads can also be achieved.</p>
<p>Chromatin immunoprecipitation (ChIP) is a method for determining transcription factor binding sites and DNA-protein interactions. It has in the past been combined with array technology (ChIP-chip) with some success. Next gen sequencing can also be applied in this area. Methylation immunoprecipitation (MeDIP) can also be performed and also on arrays.</p>
<p>The ability to learn more about methylation and TF binding sites on a genome wide scale is a valuable resource and could teach us much about disease and molecular biology in general.</p>
<h2><span id="See_also" class="mw-headline">See also</span></h2>
<ul>
<li><a title="2 Base Encoding" href="/wiki/2_Base_Encoding"><font color="#0645ad">2 Base Encoding</font></a></li>
<li><a class="mw-redirect" title="Next-generation sequencing" href="/wiki/Next-generation_sequencing"><font color="#0645ad">Next-generation sequencing</font></a></li>
<li><a title="Applied Biosystems" href="/wiki/Applied_Biosystems"><font color="#0645ad">Applied Biosystems</font></a></li>
<li><a title="Illumina (company)" href="/wiki/Illumina_(company)"><font color="#0645ad">Illumina (company)</font></a></li>
<li><a title="454 Life Sciences" href="/wiki/454_Life_Sciences"><font color="#0645ad">454 Life Sciences</font></a></li>
</ul>
<h2><span id="References" class="mw-headline">References</span></h2>
<div class="reflist references-small">
<div class="references">
<ol>
<li id="cite_note-0"><b><a href="#cite_ref-0"><font color="#0645ad">^</font></a></b> <span class="citation Journal">Valouev A, Ichikawa J, Tonthat T, <i>et al.</i> (July 2008). <a class="external text" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2493394" rel="nofollow"><font color="#3366bb">"A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning"</font></a>. <i>Genome Research</i> <b>18</b> (7): 1051–63. <a title="Digital object identifier" href="/wiki/Digital_object_identifier"><font color="#0645ad">doi</font></a>:<a class="external text" href="http://dx.doi.org/10.1101%2Fgr.076463.108" rel="nofollow"><font color="#3366bb">10.1101/gr.076463.108</font></a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a> <a class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/18477713" rel="nofollow"><font color="#3366bb">18477713</font></a>.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=A+high-resolution%2C+nucleosome+position+map+of+C.+elegans+reveals+a+lack+of+universal+sequence-dictated+positioning&rft.jtitle=Genome+Research&rft.aulast=Valouev+A%2C+Ichikawa+J%2C+Tonthat+T%2C+%27%27et+al.%27%27&rft.au=Valouev+A%2C+Ichikawa+J%2C+Tonthat+T%2C+%27%27et+al.%27%27&rft.date=July+2008&rft.volume=18&rft.issue=7&rft.pages=1051%E2%80%9363&rft_id=info:doi/10.1101%2Fgr.076463.108&rft_id=info:pmid/18477713&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"><span style="display: none"> </span></span></li>
<li id="cite_note-1"><b><a href="#cite_ref-1"><font color="#0645ad">^</font></a></b> <span class="citation Journal">Cloonan N, Forrest AR, Kolle G, <i>et al.</i> (July 2008). "Stem cell transcriptome profiling via massive-scale mRNA sequencing". <i>Nature Methods</i> <b>5</b> (7): 613–9. <a title="Digital object identifier" href="/wiki/Digital_object_identifier"><font color="#0645ad">doi</font></a>:<a class="external text" href="http://dx.doi.org/10.1038%2Fnmeth.1223" rel="nofollow"><font color="#3366bb">10.1038/nmeth.1223</font></a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a> <a class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/18516046" rel="nofollow"><font color="#3366bb">18516046</font></a>.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Stem+cell+transcriptome+profiling+via+massive-scale+mRNA+sequencing&rft.jtitle=Nature+Methods&rft.aulast=Cloonan+N%2C+Forrest+AR%2C+Kolle+G%2C+%27%27et+al.%27%27&rft.au=Cloonan+N%2C+Forrest+AR%2C+Kolle+G%2C+%27%27et+al.%27%27&rft.date=July+2008&rft.volume=5&rft.issue=7&rft.pages=613%E2%80%939&rft_id=info:doi/10.1038%2Fnmeth.1223&rft_id=info:pmid/18516046&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"><span style="display: none"> </span></span></li>
<li id="cite_note-2"><b><a href="#cite_ref-2"><font color="#0645ad">^</font></a></b> <span class="citation Journal">Tang F, Barbacioru C, Wang Y, <i>et al.</i> (May 2009). "mRNA-Seq whole-transcriptome analysis of a single cell". <i>Nature Methods</i> <b>6</b> (5): 377–82. <a title="Digital object identifier" href="/wiki/Digital_object_identifier"><font color="#0645ad">doi</font></a>:<a class="external text" href="http://dx.doi.org/10.1038%2Fnmeth.1315" rel="nofollow"><font color="#3366bb">10.1038/nmeth.1315</font></a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a> <a class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/19349980" rel="nofollow"><font color="#3366bb">19349980</font></a>.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=mRNA-Seq+whole-transcriptome+analysis+of+a+single+cell&rft.jtitle=Nature+Methods&rft.aulast=Tang+F%2C+Barbacioru+C%2C+Wang+Y%2C+%27%27et+al.%27%27&rft.au=Tang+F%2C+Barbacioru+C%2C+Wang+Y%2C+%27%27et+al.%27%27&rft.date=May+2009&rft.volume=6&rft.issue=5&rft.pages=377%E2%80%9382&rft_id=info:doi/10.1038%2Fnmeth.1315&rft_id=info:pmid/19349980&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"><span style="display: none"> </span></span></li>
<li id="cite_note-3"><b><a href="#cite_ref-3"><font color="#0645ad">^</font></a></b> <span class="citation Journal">McKernan KJ, Peckham HE, Costa GL, <i>et al.</i> (September 2009). <a class="external text" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2752135" rel="nofollow"><font color="#3366bb">"Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding"</font></a>. <i>Genome Research</i> <b>19</b> (9): 1527–41. <a title="Digital object identifier" href="/wiki/Digital_object_identifier"><font color="#0645ad">doi</font></a>:<a class="external text" href="http://dx.doi.org/10.1101%2Fgr.091868.109" rel="nofollow"><font color="#3366bb">10.1101/gr.091868.109</font></a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a> <a class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/19546169" rel="nofollow"><font color="#3366bb">19546169</font></a>.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Sequence+and+structural+variation+in+a+human+genome+uncovered+by+short-read%2C+massively+parallel+ligation+sequencing+using+two-base+encoding&rft.jtitle=Genome+Research&rft.aulast=McKernan+KJ%2C+Peckham+HE%2C+Costa+GL%2C+%27%27et+al.%27%27&rft.au=McKernan+KJ%2C+Peckham+HE%2C+Costa+GL%2C+%27%27et+al.%27%27&rft.date=September+2009&rft.volume=19&rft.issue=9&rft.pages=1527%E2%80%9341&rft_id=info:doi/10.1101%2Fgr.091868.109&rft_id=info:pmid/19546169&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"><span style="display: none"> </span></span></li>
</ol>
</div>
</div>
<h2><span id="Further_reading" class="mw-headline">Further reading</span></h2>
<ul>
<li><span class="citation Journal">Mardis ER (2008). "Next-generation DNA sequencing methods". <i>Annual Review of Genomics and Human Genetics</i> <b>9</b>: 387–402. <a title="Digital object identifier" href="/wiki/Digital_object_identifier"><font color="#0645ad">doi</font></a>:<a class="external text" href="http://dx.doi.org/10.1146%2Fannurev.genom.9.081307.164359" rel="nofollow"><font color="#3366bb">10.1146/annurev.genom.9.081307.164359</font></a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a> <a class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/18576944" rel="nofollow"><font color="#3366bb">18576944</font></a>.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Next-generation+DNA+sequencing+methods&rft.jtitle=Annual+Review+of+Genomics+and+Human+Genetics&rft.aulast=Mardis+ER&rft.au=Mardis+ER&rft.date=2008&rft.volume=9&rft.pages=387%E2%80%93402&rft_id=info:doi/10.1146%2Fannurev.genom.9.081307.164359&rft_id=info:pmid/18576944&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"><span style="display: none"> </span></span></li>
<li><span class="citation Journal">Mardis ER (2009). <a class="external text" href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2684661" rel="nofollow"><font color="#3366bb">"New strategies and emerging technologies for massively parallel sequencing: applications in medical research"</font></a>. <i>Genome Medicine</i> <b>1</b> (4): 40. <a title="Digital object identifier" href="/wiki/Digital_object_identifier"><font color="#0645ad">doi</font></a>:<a class="external text" href="http://dx.doi.org/10.1186%2Fgm40" rel="nofollow"><font color="#3366bb">10.1186/gm40</font></a>. <a class="mw-redirect" title="PubMed Identifier" href="/wiki/PubMed_Identifier"><font color="#0645ad">PMID</font></a> <a class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/19435481" rel="nofollow"><font color="#3366bb">19435481</font></a>.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=New+strategies+and+emerging+technologies+for+massively+parallel+sequencing%3A+applications+in+medical+research&rft.jtitle=Genome+Medicine&rft.aulast=Mardis+ER&rft.au=Mardis+ER&rft.date=2009&rft.volume=1&rft.issue=4&rft.pages=40&rft_id=info:doi/10.1186%2Fgm40&rft_id=info:pmid/19435481&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"><span style="display: none"> </span></span></li>
</ul>
<h2><span id="External_links" class="mw-headline">External links</span></h2>
<ul>
<li><span class="citation web"><a class="external text" href="http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_061241.pdf" rel="nofollow"><font color="#3366bb">"The SOLiD 3 System: Enabling the Next Generation of Science"</font></a>. <a title="Life Technologies" href="/wiki/Life_Technologies"><font color="#0645ad">Life Technologies</font></a>. 2009<span class="printonly">. <a class="external free" href="http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_061241.pdf" rel="nofollow"><font color="#3366bb">http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_061241.pdf</font></a></span><span class="reference-accessdate">. Retrieved January 27, 2010</span>.</span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=bookitem&rft.btitle=The+SOLiD+3+System%3A+Enabling+the+Next+Generation+of+Science&rft.atitle=&rft.date=2009&rft.pub=%5B%5BLife+Technologies%5D%5D&rft_id=http%3A%2F%2Fwww3.appliedbiosystems.com%2Fcms%2Fgroups%2Fmcb_marketing%2Fdocuments%2Fgeneraldocuments%2Fcms_061241.pdf&rfr_id=info:sid/en.wikipedia.org:ABI_Solid_Sequencing"><span style="display: none"> </span></span></li>
<li><span class="citation web"><a class="external text" href="http://marketing.appliedbiosystems.com/mk/get/SOLID_ACCURACY_Landing?CID=BN-88889-NAHomePage" rel="nofollow"><font color="#3366bb">"The SOLiD 3 Plus System"</font></a>. <a title="Life Technologies" href="/wiki/Life_Technologies"><font color="#0645ad">Life Technologies</font></a>. 2009<span class="printonly">. <a class="external free" href="http://marketing.appliedbiosystems.com/mk/get/SOLID_ACCURACY_Landing?CID=BN-88889-NAHomePage" rel="nofollow"><font color="#3366bb">http://marketing.appliedbiosystems.com/mk/get/SOLID_ACCURACY_Landing?CID=BN-88889-NAHomePage</font></a></span><span class="reference-accessdate">. Retrieved January 27, 2010</span>.</span></li>
</ul>
