Selection:Article Title: HIV Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical Commercial Assays Superscript III 1st strand Invitrogen Cat#18080051 Platinum Taq PCR polymerase Invitrogen Cat#10966083 E-Gel 96 well 1% agarose Thermo Fisher Scientific Cat#G700801 Oligonucleotides E20 F 5’GGGCCACACATGCCTGTGTACCCACAG 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E115 5’ GAAAAATTCCCCTCCACAATTAA 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E30 F 5’GTGTACCCACAGACCCCAGCCCACAAG3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E125 R 5’CAATTTCTGGGTCCCCTCCTGAGG 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A Deposited Data RNA and DNA sequencing Genbank MH642355 RNA and DNA sequencing Genbank MH642607 RNA and DNA sequencing Genbank MH642608 RNA and DNA sequencing Genbank MH643062 RNA and DNA sequencing Genbank MH643063 RNA and DNA sequencing Genbank MH643573 Software and Algorithms Subtype analyses Smartgene, Lausanne, Switzerland https://www.smartgene.com/ Viral Tropism Web PSSM, Mullins lab, University of Washington https://indra.mullins.microbiol.washington. edu/webpssm/ Flow Jo software BD Biosciences https://www.flowjo.com/ Perl script language Perl https://www.perl.org/ MUSCLE Edgar, 2004 http://www.megasoftware.net/ MAFFT Katoh and Standley, 2013 https://mafft.cbrc.jp/alignment/software/ Aliview Larsson, 2014 www.ormbunkar.se/aliview/downloads RDP4 Martin et al., 2015 http://web.cbio.uct.ac.za/ darren/rdp.html Translator X Abascal et al., 2010 http://www.translatorx.co.uk/ PhyML v3.0 Guindon and Gascuel, 2003 https://github.com/stephaneguindon/phyml/ BaTS Parker et al., 2008 http://evolve.zoo.ox.ac.uk/Evolve/BaTS.html Mr Bayes v3.6.2 Ronquist et al., 2012 http://nbisweden.github.io/MrBayes/ download.html Tracer BEAST https://github.com/beast-dev/tracer/releases/ tag/v1.7.1 Biopython Cock et al., 2009 https://biopython.org/wiki/Download Elim Dupes Los Alamos HIV Database http://www.hiv.lanl.gov R: A language and environment for statistical computing.
Staining:Article Title: HIV Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical Commercial Assays Superscript III 1st strand Invitrogen Cat#18080051 Platinum Taq PCR polymerase Invitrogen Cat#10966083 E-Gel 96 well 1% agarose Thermo Fisher Scientific Cat#G700801 Oligonucleotides E20 F 5’GGGCCACACATGCCTGTGTACCCACAG 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E115 5’ GAAAAATTCCCCTCCACAATTAA 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E30 F 5’GTGTACCCACAGACCCCAGCCCACAAG3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E125 R 5’CAATTTCTGGGTCCCCTCCTGAGG 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A Deposited Data RNA and DNA sequencing Genbank MH642355 RNA and DNA sequencing Genbank MH642607 RNA and DNA sequencing Genbank MH642608 RNA and DNA sequencing Genbank MH643062 RNA and DNA sequencing Genbank MH643063 RNA and DNA sequencing Genbank MH643573 Software and Algorithms Subtype analyses Smartgene, Lausanne, Switzerland https://www.smartgene.com/ Viral Tropism Web PSSM, Mullins lab, University of Washington https://indra.mullins.microbiol.washington. edu/webpssm/ Flow Jo software BD Biosciences https://www.flowjo.com/ Perl script language Perl https://www.perl.org/ MUSCLE Edgar, 2004 http://www.megasoftware.net/ MAFFT Katoh and Standley, 2013 https://mafft.cbrc.jp/alignment/software/ Aliview Larsson, 2014 www.ormbunkar.se/aliview/downloads RDP4 Martin et al., 2015 http://web.cbio.uct.ac.za/ darren/rdp.html Translator X Abascal et al., 2010 http://www.translatorx.co.uk/ PhyML v3.0 Guindon and Gascuel, 2003 https://github.com/stephaneguindon/phyml/ BaTS Parker et al., 2008 http://evolve.zoo.ox.ac.uk/Evolve/BaTS.html Mr Bayes v3.6.2 Ronquist et al., 2012 http://nbisweden.github.io/MrBayes/ download.html Tracer BEAST https://github.com/beast-dev/tracer/releases/ tag/v1.7.1 Biopython Cock et al., 2009 https://biopython.org/wiki/Download Elim Dupes Los Alamos HIV Database http://www.hiv.lanl.gov R: A language and environment for statistical computing.
Blocking Assay:Article Title: HIV Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical Commercial Assays Superscript III 1st strand Invitrogen Cat#18080051 Platinum Taq PCR polymerase Invitrogen Cat#10966083 E-Gel 96 well 1% agarose Thermo Fisher Scientific Cat#G700801 Oligonucleotides E20 F 5’GGGCCACACATGCCTGTGTACCCACAG 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E115 5’ GAAAAATTCCCCTCCACAATTAA 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E30 F 5’GTGTACCCACAGACCCCAGCCCACAAG3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E125 R 5’CAATTTCTGGGTCCCCTCCTGAGG 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A Deposited Data RNA and DNA sequencing Genbank MH642355 RNA and DNA sequencing Genbank MH642607 RNA and DNA sequencing Genbank MH642608 RNA and DNA sequencing Genbank MH643062 RNA and DNA sequencing Genbank MH643063 RNA and DNA sequencing Genbank MH643573 Software and Algorithms Subtype analyses Smartgene, Lausanne, Switzerland https://www.smartgene.com/ Viral Tropism Web PSSM, Mullins lab, University of Washington https://indra.mullins.microbiol.washington. edu/webpssm/ Flow Jo software BD Biosciences https://www.flowjo.com/ Perl script language Perl https://www.perl.org/ MUSCLE Edgar, 2004 http://www.megasoftware.net/ MAFFT Katoh and Standley, 2013 https://mafft.cbrc.jp/alignment/software/ Aliview Larsson, 2014 www.ormbunkar.se/aliview/downloads RDP4 Martin et al., 2015 http://web.cbio.uct.ac.za/ darren/rdp.html Translator X Abascal et al., 2010 http://www.translatorx.co.uk/ PhyML v3.0 Guindon and Gascuel, 2003 https://github.com/stephaneguindon/phyml/ BaTS Parker et al., 2008 http://evolve.zoo.ox.ac.uk/Evolve/BaTS.html Mr Bayes v3.6.2 Ronquist et al., 2012 http://nbisweden.github.io/MrBayes/ download.html Tracer BEAST https://github.com/beast-dev/tracer/releases/ tag/v1.7.1 Biopython Cock et al., 2009 https://biopython.org/wiki/Download Elim Dupes Los Alamos HIV Database http://www.hiv.lanl.gov R: A language and environment for statistical computing.
Recombinant:Article Title: HIV Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical Commercial Assays Superscript III 1st strand Invitrogen Cat#18080051 Platinum Taq PCR polymerase Invitrogen Cat#10966083 E-Gel 96 well 1% agarose Thermo Fisher Scientific Cat#G700801 Oligonucleotides E20 F 5’GGGCCACACATGCCTGTGTACCCACAG 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E115 5’ GAAAAATTCCCCTCCACAATTAA 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E30 F 5’GTGTACCCACAGACCCCAGCCCACAAG3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E125 R 5’CAATTTCTGGGTCCCCTCCTGAGG 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A Deposited Data RNA and DNA sequencing Genbank MH642355 RNA and DNA sequencing Genbank MH642607 RNA and DNA sequencing Genbank MH642608 RNA and DNA sequencing Genbank MH643062 RNA and DNA sequencing Genbank MH643063 RNA and DNA sequencing Genbank MH643573 Software and Algorithms Subtype analyses Smartgene, Lausanne, Switzerland https://www.smartgene.com/ Viral Tropism Web PSSM, Mullins lab, University of Washington https://indra.mullins.microbiol.washington. edu/webpssm/ Flow Jo software BD Biosciences https://www.flowjo.com/ Perl script language Perl https://www.perl.org/ MUSCLE Edgar, 2004 http://www.megasoftware.net/ MAFFT Katoh and Standley, 2013 https://mafft.cbrc.jp/alignment/software/ Aliview Larsson, 2014 www.ormbunkar.se/aliview/downloads RDP4 Martin et al., 2015 http://web.cbio.uct.ac.za/ darren/rdp.html Translator X Abascal et al., 2010 http://www.translatorx.co.uk/ PhyML v3.0 Guindon and Gascuel, 2003 https://github.com/stephaneguindon/phyml/ BaTS Parker et al., 2008 http://evolve.zoo.ox.ac.uk/Evolve/BaTS.html Mr Bayes v3.6.2 Ronquist et al., 2012 http://nbisweden.github.io/MrBayes/ download.html Tracer BEAST https://github.com/beast-dev/tracer/releases/ tag/v1.7.1 Biopython Cock et al., 2009 https://biopython.org/wiki/Download Elim Dupes Los Alamos HIV Database http://www.hiv.lanl.gov R: A language and environment for statistical computing.
Lysis:Article Title: HIV Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical Commercial Assays Superscript III 1st strand Invitrogen Cat#18080051 Platinum Taq PCR polymerase Invitrogen Cat#10966083 E-Gel 96 well 1% agarose Thermo Fisher Scientific Cat#G700801 Oligonucleotides E20 F 5’GGGCCACACATGCCTGTGTACCCACAG 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E115 5’ GAAAAATTCCCCTCCACAATTAA 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E30 F 5’GTGTACCCACAGACCCCAGCCCACAAG3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E125 R 5’CAATTTCTGGGTCCCCTCCTGAGG 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A Deposited Data RNA and DNA sequencing Genbank MH642355 RNA and DNA sequencing Genbank MH642607 RNA and DNA sequencing Genbank MH642608 RNA and DNA sequencing Genbank MH643062 RNA and DNA sequencing Genbank MH643063 RNA and DNA sequencing Genbank MH643573 Software and Algorithms Subtype analyses Smartgene, Lausanne, Switzerland https://www.smartgene.com/ Viral Tropism Web PSSM, Mullins lab, University of Washington https://indra.mullins.microbiol.washington. edu/webpssm/ Flow Jo software BD Biosciences https://www.flowjo.com/ Perl script language Perl https://www.perl.org/ MUSCLE Edgar, 2004 http://www.megasoftware.net/ MAFFT Katoh and Standley, 2013 https://mafft.cbrc.jp/alignment/software/ Aliview Larsson, 2014 www.ormbunkar.se/aliview/downloads RDP4 Martin et al., 2015 http://web.cbio.uct.ac.za/ darren/rdp.html Translator X Abascal et al., 2010 http://www.translatorx.co.uk/ PhyML v3.0 Guindon and Gascuel, 2003 https://github.com/stephaneguindon/phyml/ BaTS Parker et al., 2008 http://evolve.zoo.ox.ac.uk/Evolve/BaTS.html Mr Bayes v3.6.2 Ronquist et al., 2012 http://nbisweden.github.io/MrBayes/ download.html Tracer BEAST https://github.com/beast-dev/tracer/releases/ tag/v1.7.1 Biopython Cock et al., 2009 https://biopython.org/wiki/Download Elim Dupes Los Alamos HIV Database http://www.hiv.lanl.gov R: A language and environment for statistical computing.
Polymerase Chain Reaction:Article Title: HIV Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Critical Commercial Assays Superscript III 1st strand Invitrogen Cat#18080051 Platinum Taq PCR polymerase Invitrogen Cat#10966083 E-Gel 96 well 1% agarose Thermo Fisher Scientific Cat#G700801 Oligonucleotides E20 F 5’GGGCCACACATGCCTGTGTACCCACAG 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E115 5’ GAAAAATTCCCCTCCACAATTAA 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E30 F 5’GTGTACCCACAGACCCCAGCCCACAAG3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A E125 R 5’CAATTTCTGGGTCCCCTCCTGAGG 3’ Josefsson et al., 2012; von Stockenstrom et al., 2015 N/A Deposited Data RNA and DNA sequencing Genbank MH642355 RNA and DNA sequencing Genbank MH642607 RNA and DNA sequencing Genbank MH642608 RNA and DNA sequencing Genbank MH643062 RNA and DNA sequencing Genbank MH643063 RNA and DNA sequencing Genbank MH643573 Software and Algorithms Subtype analyses Smartgene, Lausanne, Switzerland https://www.smartgene.com/ Viral Tropism Web PSSM, Mullins lab, University of Washington https://indra.mullins.microbiol.washington. edu/webpssm/ Flow Jo software BD Biosciences https://www.flowjo.com/ Perl script language Perl https://www.perl.org/ MUSCLE Edgar, 2004 http://www.megasoftware.net/ MAFFT Katoh and Standley, 2013 https://mafft.cbrc.jp/alignment/software/ Aliview Larsson, 2014 www.ormbunkar.se/aliview/downloads RDP4 Martin et al., 2015 http://web.cbio.uct.ac.za/ darren/rdp.html Translator X Abascal et al., 2010 http://www.translatorx.co.uk/ PhyML v3.0 Guindon and Gascuel, 2003 https://github.com/stephaneguindon/phyml/ BaTS Parker et al., 2008 http://evolve.zoo.ox.ac.uk/Evolve/BaTS.html Mr Bayes v3.6.2 Ronquist et al., 2012 http://nbisweden.github.io/MrBayes/ download.html Tracer BEAST https://github.com/beast-dev/tracer/releases/ tag/v1.7.1 Biopython Cock et al., 2009 https://biopython.org/wiki/Download Elim Dupes Los Alamos HIV Database http://www.hiv.lanl.gov R: A language and environment for statistical computing.
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